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In molecular biology, the dipeptidyl-peptidase IV family is a family of serine peptidases which belong to MEROPS peptidase family S9 (clan SC), subfamily S9B (dipeptidyl-peptidase IV). The protein fold of the peptidase domain for members of this family resembles that of serine carboxypeptidase D, the type example of clan SC. The type example of this family is Dipeptidyl peptidase-4.Human proteins in this family are: Dipeptidyl peptidase-4 Dipeptidyl peptidase 8 Dipeptidyl peptidase 9 Inactive dipeptidyl peptidase 10 Dipeptidyl aminopeptidase-like protein 6 Seprase | https://en.wikipedia.org/wiki/Dipeptidyl-peptidase_IV_family |
In molecular biology, the domain B, refers to the immunoglobulin-binding domain found in the Staphylococcus aureus virulence factor protein A (SpA). Hence, it is abbreviated to SpAB. | https://en.wikipedia.org/wiki/SpAB_protein_domain |
In molecular biology, the eIF-W2 domain functions as the binding site for Mnk eIF4E kinase, an enzyme that phosphorylates eukaryotic initiation factor 4E (eIF4E). For eIF2B-epsilon, the W2 C-terminal domain functions in guanine nucleotide exchange on eIF2. For eIF5, the W2 domain functions in mediating the multifactor complex (MFC) formation with eIF1, eIF2-GTP, eIF3 and Met-tRNAiMet. The eIF5 W2 C-terminal domain and the adjacent N-terminal linker region is responsible for the GDI activity against eIF2-GDP. | https://en.wikipedia.org/wiki/EIF-W2_protein_domain |
In molecular biology, the electroneutral cation-Cl (electroneutral potassium chloride cotransporter) family of proteins are a family of solute carrier proteins. This family includes the products of the Human genes: SLC12A1, SLC12A1, SLC12A2, SLC12A3, SLC12A4, SLC12A5, SLC12A6, SLC12A7, SLC12A8 and SLC12A9. The K-Cl co-transporter (KCC) mediates the coupled movement of K+ and Cl− ions across the plasma membrane of many animal cells. This transport is involved in the regulatory volume decrease in response to cell swelling in red blood cells, and has been proposed to play a role in the vectorial movement of Cl− across kidney epithelia. | https://en.wikipedia.org/wiki/Electroneutral_cation-Cl |
The transport process involves one for one electroneutral movement of K+ together with Cl−, and, in all known mammalian cells, the net movement is outward.The neuronal KCC subtype KCC2 is cell-volume insensitive and plays a unique role in maintaining low intracellular Cl−concentration, which is required in neurones for the functioning of Cl− dependent fast synaptic inhibition, mediated by certain neurotransmitters, such as gamma-aminobutyric acid (GABA) and glycine. Three isoforms of the K-Cl co-transporter have been described, termed KCC1 (SLC12A4), KCC2 (SLC12A5), and KCC3 (SLC12A6), containing 1085, 1116 and 1150 amino acids, respectively. They are predicted to have 12 transmembrane (TM) regions in a central hydrophobic domain, together with hydrophilic N- and C-termini that are likely cytoplasmic. | https://en.wikipedia.org/wiki/Electroneutral_cation-Cl |
Comparison of their sequences with those of other ion-transporting membrane proteins reveals that they are part of a new superfamily of cation-chloride co-transporters, which includes the Na-Cl and Na-K-2Cl co-transporters. KCC1 and KCC3 are widely expressed in human tissues, while KCC2 is expressed only in brain neurons, making it likely that this is the isoform responsible for maintaining low Cl− concentration in neurons. A study in the model organism C. elegans found that the KCC3 ortholog functions in glial cells to regulate animal behavior.KCC1 is widely expressed in human tissues, and when heterologously expressed, possesses the functional characteristics of the well-studied red blood cell K-Cl co-transporter, including stimulation by both swelling and N-ethylmaleimide. | https://en.wikipedia.org/wiki/Electroneutral_cation-Cl |
Several splice variants have also been identified. KCC3 is widely expressed in human tissues and, like KCC1, is stimulated by both swelling and N-ethylmaleimide. | https://en.wikipedia.org/wiki/Electroneutral_cation-Cl |
The induction of KCC3 is up-regulated by vascular endothelial growth factor and down-regulated by tumour necrosis factor. Defects in KCC3 are linked to agenesis of the corpus callosum with peripheral neuropathy. This disorder is characterised by severe progressive sensorimotor neuropathy, mental retardation, dysmorphic features and complete or partial agenesis of the corpus callosum. == References == | https://en.wikipedia.org/wiki/Electroneutral_cation-Cl |
In molecular biology, the engrailed homeobox proteins are a family of homeobox proteins which are characterised by the presence of a region of some 20 amino-acid residues located at the C-terminal of the 'homeobox' domain. This region forms a signature pattern for this subfamily of proteins. == References == | https://en.wikipedia.org/wiki/Engrailed_homeobox_protein |
In molecular biology, the enteroviral 3′ UTR element is an RNA structure found in the 3′ UTR of various enteroviruses. The overall structure forms the origin of replication (OriR) for the initiation of (-) strand RNA synthesis. Pseudoknots have also been predicted in this structure. | https://en.wikipedia.org/wiki/Enteroviral_3′_UTR_element |
In molecular biology, the epsilon antitoxin, produced by various prokaryotes, forms part of a post-segregational killing system, which is involved in the initiation of programmed cell death of plasmid-free cells. The protein is folded into a three-helix bundle that directly interacts with the zeta toxin, inactivating it. == References == | https://en.wikipedia.org/wiki/Epsilon_antitoxin |
In molecular biology, the eukaryotic translation initiation factor 4E family (eIF-4E) is a family of proteins that bind to the cap structure of eukaryotic cellular mRNAs. Members of this family recognise and bind the 7-methyl-guanosine-containing (m7Gppp) cap during an early step in the initiation of protein synthesis and facilitate ribosome binding to an mRNA by inducing the unwinding of its secondary structures. A tryptophan in the central part of the sequence of human eIF-4E seems to be implicated in cap-binding.Members of this family include EIF4E, EIF4E2, EIF4E3 and EIF4E1B. | https://en.wikipedia.org/wiki/Eukaryotic_translation_initiation_factor_4E_family |
In molecular biology, the fasciclin domain (FAS1 domain) is an extracellular domain of about 140 amino acid residues. It has been suggested that the FAS1 domain represents an ancient cell adhesion domain common to plants and animals; related FAS1 domains are also found in bacteria.The crystal structure of FAS1 domains 3 and 4 of fasciclin I from Drosophila melanogaster (Fruit fly) has been determined, revealing a novel domain fold consisting of a seven-stranded beta wedge and at least five alpha helices; two well-ordered N-acetylglucosamine groups attached to a conserved asparagine are located in the interface region between the two FAS1 domains. Fasciclin I is an insect neural cell adhesion molecule involved in axonal guidance that is attached to the membrane by a GPI-anchored protein. FAS1 domains are present in many secreted and membrane-anchored proteins. | https://en.wikipedia.org/wiki/Fasciclin_domain |
These proteins are usually GPI anchored and consist of: (i) a single FAS1 domain, (ii) a tandem array of FAS1 domains, or (iii) FAS1 domain(s) interspersed with other domains. Proteins known to contain a FAS1 domain include: Fasciclin I (4 FAS1 domains). Human TGF-beta induced Ig-H3 (BIgH3) protein (4 FAS1 domains), where the FAS1 domains mediate cell adhesion through an interaction with alpha3/beta1 integrin; mutation in the FAS1 domains result in corneal dystrophy. | https://en.wikipedia.org/wiki/Fasciclin_domain |
Volvox major cell adhesion protein (2 FAS1 domains). Arabidopsis thaliana fasciclin-like arabinogalactan proteins (2 FAS1 domains). Mammalian stabilin protein, a family of fasciclin-like hyaluronan receptor homologues (7 FAS1 domains). | https://en.wikipedia.org/wiki/Fasciclin_domain |
Human extracellular matrix protein periostin (4 FAS1 domains). Bacterial immunogenic protein MPT70 (1 FAS1 domain).The FAS1 domains of both human periostin and BIgH3 proteins were found to contain vitamin K-dependent gamma-carboxyglutamate residues. Gamma-carboxyglutamate residues are more commonly associated with GLA domains, where they occur through post-translational modification catalysed by the vitamin K-dependent enzyme gamma-glutamylcarboxylase. | https://en.wikipedia.org/wiki/Fasciclin_domain |
In molecular biology, the fatty acid metabolism regulator protein FadR, is a bacterial transcription factor. Bacteria regulate membrane fluidity by manipulating the relative levels of saturated and unsaturated fatty acids within the phospholipids of their membrane bilayers. In Escherichia coli, the transcription factor, FadR, functions as a switch that co-ordinately regulates the machinery required for fatty acid beta-oxidation and the expression of a key enzyme in fatty acid biosynthesis. | https://en.wikipedia.org/wiki/Fatty_acid_metabolism_regulator_protein_FadR |
This single [repressor controls the transcription of the whole fad regulon. Binding of fadR is specifically inhibited by long chain fatty acyl-CoA compounds. The crystal structure of FadR reveals a two domain dimeric molecule where the N-terminal winged-helix domain binds DNA, and the C-terminal domain binds acyl-CoA. | https://en.wikipedia.org/wiki/Fatty_acid_metabolism_regulator_protein_FadR |
The binding of acyl-CoA to the C-terminal domain results in a conformational change that affects the DNA binding affinity of the N-terminal domain.FadR is a member of the GntR family of bacterial transcription regulators. The DNA-binding domain is well conserved for this family, whereas the C-terminal effector-binding domain is more variable, and is consequently used to define the GntR subfamilies. The FadR group is the largest subgroup, and is characterised by an all-helical C-terminal domain composed of 6 to 7 alpha helices. == References == | https://en.wikipedia.org/wiki/Fatty_acid_metabolism_regulator_protein_FadR |
In molecular biology, the ferric uptake regulator family is a family of bacterial proteins involved in regulating metal ion uptake and in metal homeostasis. The family is named for its founding member, known as the ferric uptake regulator or ferric uptake regulatory protein (Fur). Fur proteins are responsible for controlling the intracellular concentration of iron in many bacteria. Iron is essential for most organisms, but its concentration must be carefully managed over a wide range of environmental conditions; high concentrations can be toxic due to the formation of reactive oxygen species. | https://en.wikipedia.org/wiki/Ferric_uptake_regulator_family |
In molecular biology, the five-prime cap (5′ cap) is a specially altered nucleotide on the 5′ end of some primary transcripts such as precursor messenger RNA. This process, known as mRNA capping, is highly regulated and vital in the creation of stable and mature messenger RNA able to undergo translation during protein synthesis. Mitochondrial mRNA and chloroplastic mRNA are not capped. | https://en.wikipedia.org/wiki/Five-prime_cap |
In molecular biology, the flagellar motor switch protein (Flig) is one of three proteins in certain bacteria coded for by the gene fliG. The other two proteins are FliN coded for by fliN, and FliM coded for by fliM. The protein complex regulates the direction of flagellar rotation and hence controls swimming behaviour. The switch is a complex apparatus that responds to signals transduced by the chemotaxis sensory signalling system during chemotactic behaviour. CheY, the chemotaxis response regulator, is believed to act directly on the switch to induce a switch in the flagellar motor direction of rotation. | https://en.wikipedia.org/wiki/Flagellar_motor_switch_protein |
In molecular biology, the forkhead-associated domain (FHA domain) is a phosphopeptide recognition domain found in many regulatory proteins. It displays specificity for phosphothreonine-containing epitopes but will also recognise phosphotyrosine with relatively high affinity. It spans approximately 80-100 amino acid residues folded into an 11-stranded beta sandwich, which sometimes contains small helical insertions between the loops connecting the strands.To date, genes encoding FHA-containing proteins have been identified in eubacterial, eukaryotic and archaeal genomes. The domain is present in a diverse range of proteins, such as kinases, phosphatases, kinesins, transcription factors, RNA-binding proteins and metabolic enzymes which partake in many different cellular processes - DNA repair, signal transduction, vesicular transport and protein degradation are just a few examples. | https://en.wikipedia.org/wiki/Forkhead-associated_domain |
In molecular biology, the frataxin-like domain is a protein domain found in proteins including eukaryotic frataxin and bacterial CyaY. The bacterial CyaY proteins are iron-sulphur cluster (FeS) metabolism proteins which are homologous to eukaryotic frataxin. Partial phylogenetic profiling suggests that CyaY most likely functions as part of the ISC system for FeS cluster biosynthesis, and is supported by experimental data in some species. == References == | https://en.wikipedia.org/wiki/Frataxin-like_domain |
In molecular biology, the fungal fruit body lectin family consists of several fungal fruit body lectin proteins. Fruit body lectins are thought to have insecticidal activity and may also function in capturing nematodes. One member of this family, the lectin XCL from Boletus chrysenteron (formerly Xerocomus chrysenteron), induces drastic changes in the actin cytoskeleton after sugar binding at the cell surface and internalisation, and has potent insecticidal activity. The fold of lectin XCL is not related to any of several other lectin folds, but shows significant structural similarity to cytolysins. == References == | https://en.wikipedia.org/wiki/Fungal_fruit_body_lectin_family |
In molecular biology, the fungal fucose-specific lectin family is a family of lectins. Lectins are proteins which are involved in many recognition events at the molecular or cellular level. These fungal lectins, such as Aleuria aurantia lectin AAL, specifically recognise fucosylated glycans. AAL is a dimeric protein, with each monomer being organised into a six-bladed beta-propeller fold and a small antiparallel two-stranded beta-sheet. | https://en.wikipedia.org/wiki/Fungal_fucose-specific_lectin |
The beta-propeller fold is important in fucose recognition; five binding pockets are found between the propeller blades. The small beta-sheet, on the other hand, is involved in the dimerisation process. == References == | https://en.wikipedia.org/wiki/Fungal_fucose-specific_lectin |
In molecular biology, the galactose binding lectin domain is a protein domain. It is found in many proteins including the lectin purified from sea urchin (Anthocidaris crassispina) eggs, SUEL. This lectin exists as a disulfide-linked homodimer of two subunits; the dimeric form is essential for hemagglutination activity. The sea urchin egg lectin (SUEL) forms a new class of lectins. | https://en.wikipedia.org/wiki/Galactose_binding_lectin_domain |
Although SUEL was first isolated as a D-galactoside binding lectin, it was later shown that it binds to L-rhamnose preferentially. L-rhamnose and D-galactose share the same hydroxyl group orientation at C2 and C4 of the pyranose ring structure. A cysteine-rich domain (the galactose binding lectin domain) homologous to the SUEL protein has been identified in the following proteins: Plant beta-galactosidases EC 3.2.1.23 (lactases). | https://en.wikipedia.org/wiki/Galactose_binding_lectin_domain |
Mammalian latrophilin, the calcium independent receptor of alpha-latrotoxin (CIRL). The galactose-binding lectin domain is not required for alpha-latratoxin binding.Human latrophilin-1. Human Latrophilin-2. | https://en.wikipedia.org/wiki/Galactose_binding_lectin_domain |
Rhamnose-binding lectin (SAL) from catfish (Silurus asotus) eggs. This protein is composed of three tandem repeat domains homologous to the SUEL lectin domain. All cysteine positions of each domain are completely conserved. The hypothetical B0457.1, F32A7.3A and F32A7.3B proteins from Caenorhabditis elegans. == References == | https://en.wikipedia.org/wiki/Galactose_binding_lectin_domain |
In molecular biology, the glucose-methanol-choline oxidoreductase family (GMC oxidoreductase) is a family of enzymes with oxidoreductase activity. The glucose-methanol-choline (GMC) oxidoreductases are FAD flavoproteins oxidoreductases. These enzymes include a variety of proteins; choline dehydrogenase (CHD) EC 1.1.99.1, methanol oxidase (MOX) EC 1.1.3.13 and cellobiose dehydrogenase EC 1.1.99.18 which share a number of regions of sequence similarities. | https://en.wikipedia.org/wiki/Glucose-methanol-choline_oxidoreductase_family |
They contain two conserved protein domains. The N-terminal domain corresponds to the FAD ADP-binding domain, the C-terminal domain is a steroid-binding domain. == References == | https://en.wikipedia.org/wiki/Glucose-methanol-choline_oxidoreductase_family |
In molecular biology, the glutaredoxin 2 family is a family of bacterial glutaredoxins. Unlike other glutaredoxins, glutaredoxin 2 (Grx2) cannot reduce ribonucleotide reductase. Grx2 has significantly higher catalytic activity in the reduction of mixed disulphides with glutathione (GSH) compared with other glutaredoxins. The active site residues (Cys9-Pro10-Tyr11-Cys12, in Escherichia coli Grx2, which are found at the interface between the N- and C-terminal domains are identical to other glutaredoxins, but there is no other similarity between glutaredoxin 2 and other glutaredoxins. | https://en.wikipedia.org/wiki/Glutaredoxin_2_(bacterial) |
Grx2 is structurally similar to glutathione-S-transferases (GST), but there is no obvious sequence similarity. The inter-domain contacts are mainly hydrophobic, suggesting that the two domains are unlikely to be stable on their own. Both domains are needed for correct folding and activity of Grx2. | https://en.wikipedia.org/wiki/Glutaredoxin_2_(bacterial) |
It is thought that the primary function of Grx2 is to catalyse reversible glutathionylation of proteins with GSH in cellular redox regulation including the response to oxidative stress. These enzymes are not related to GLRX2. == References == | https://en.wikipedia.org/wiki/Glutaredoxin_2_(bacterial) |
In molecular biology, the glycoside hydrolase family 53 is a family of glycoside hydrolases EC 3.2.1., which are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycoside hydrolases, based on sequence similarity, has led to the definition of >100 different families. This classification is available on the CAZy web site, and also discussed at CAZypedia, an online encyclopedia of carbohydrate active enzymes.These enzymes are endo-1,4- beta-galactanases EC 3.2.1.89. The structure of this domain is known and has a TIM barrel fold. == References == | https://en.wikipedia.org/wiki/Glycoside_hydrolase_family_53 |
In molecular biology, the group I pyridoxal-dependent decarboxylases, also known as glycine cleavage system P-proteins, are a family of enzymes consisting of glycine cleavage system P-proteins (glycine dehydrogenase (decarboxylating)) EC 1.4.4.2 from bacterial, mammalian and plant sources. The P protein is part of the glycine decarboxylase multienzyme complex (GDC) also annotated as glycine cleavage system or glycine synthase. The P protein binds the alpha-amino group of glycine through its pyridoxal phosphate cofactor, carbon dioxide is released and the remaining methylamine moiety is then transferred to the lipoamide cofactor of the H protein. GDC consists of four proteins P, H, L and T.Pyridoxal-5'-phosphate-dependent amino acid decarboxylases can be divided into four groups based on amino acid sequence. Group I comprises glycine decarboxylases. | https://en.wikipedia.org/wiki/Group_I_pyridoxal-dependent_decarboxylases |
In molecular biology, the guanylate-binding proteins family is a family of GTPases that is induced by interferon (IFN)-gamma. GTPases induced by IFN-gamma (Interferon-inducible GTPase) are key to the protective immunity against microbial and viral pathogens. These GTPases are classified into three groups: the small 47-KD immunity-related GTPases (IRGs), the Mx proteins (MX1, MX2), and the large 65- to 67-kd GTPases. | https://en.wikipedia.org/wiki/Guanylate-binding_protein |
Guanylate-binding proteins (GBP) fall into the last class. GBP genes have been universally recognized in mammalian as well as in most other vertebrate genomes. A single cluster of seven human GBP genes (GBP1-GBP7) is found on chromosome 1q22.2. | https://en.wikipedia.org/wiki/Guanylate-binding_protein |
Unlike humans, in genetically controllable disease models such as mice and zebrafish, members of the GBPs gene family are organized in more than one cluster, in this case, 11 (Gbp2b- Gbp110 and 4 genes (Gbp1-Gbp4), respectively. Examinations of GBP-related sequences have shown that zebrafish gbp3 and gbp4 contain an additional function to find (FIIND) and a caspase recruitment (CARD) domains that resemble those found within the inflammasome-related proteins: Apoptosis-associated speck-like protein containing a CARD (PYCARD) and NLR Family Pyrin Domain Containing 1 (NLRP1).Structurally, GBPs consist of two domains: a globular N- terminal domain harboring the GTPase function, and an extended C- terminal helical domain. In addition, some members of the GBPs family harbor motifs (e.g., CaaX motifs) or additional domains that are thought to operate in protein-protein or protein-membrane interactions.Some GBPs have exhibited the ability to bind not only guanosine triphosphate (GTP) to produce guanosine diphosphate (GDP) but also GDP to produce guanosine monophosphate (GMP) with equimolar affinity and high intrinsic rates of hydrolyzation. | https://en.wikipedia.org/wiki/Guanylate-binding_protein |
The physiological relevance of the GBP's GDPase activity might yield important insights to elucidate GBP-specific defensive profile versus other INF-induced GTPases(e.g.IRGs). Evidence has suggested GBPs as important players in a variety of disease conditions ranging from infectious and metabolic inflammatory diseases to cancer, In the context of cell protection against bacteria, early efforts conducting loss-function assays revealed a reduced host resistance to several pathogens when lacking GBPs. More recent studies have indicated that GBPs appear to be an agent that disturbs the structural integrity of bacteria, stimulates inflammasome signaling, forms complexes on pathogen-containing vesicles in infected cells, and fosters autophagy and oxidative mechanisms helping pathogen clearance.Human GBP1 is secreted from cells without the need of a leader peptide, and has been shown to exhibit antiviral activity against Vesicular stomatitis virus and Encephalomyocarditis virus, as well as being able to regulate the inhibition of proliferation and invasion of endothelial cells in response to IFN-gamma. == References == | https://en.wikipedia.org/wiki/Guanylate-binding_protein |
In molecular biology, the haemagglutination activity domain is a conserved protein domain found near the N terminus of a number of large, repetitive bacterial proteins, including many proteins of over 2500 amino acids. A number of the members of this family have been designated adhesins, filamentous haemagglutinins, haem/haemopexin-binding protein, etc. Members generally have a signal sequence, then an intervening region, then the region described in this entry. Following this region, proteins typically have regions rich in repeats but may show no homology between the repeats of one member and the repeats of another. This domain is suggested to be a carbohydrate-dependent haemagglutination activity site.In Bordetella pertussis, the infectious agent in childhood whooping cough, filamentous haemagglutinin (FHA) is a surface-exposed and secreted protein that acts as a major virulence attachment factor, functioning as both a primary adhesin and an immunomodulator to bind the bacterial to cells of the respiratory epithelium. | https://en.wikipedia.org/wiki/Haemagglutination_activity_domain |
The FHA molecule has a globular head that consists of two domains: a shaft and a flexible tail. Its sequence contains two regions of tandem 19-residue repeats, where the repeat motif consists of short beta-strands separated by beta-turns. == References == | https://en.wikipedia.org/wiki/Haemagglutination_activity_domain |
In molecular biology, the haemolymph juvenile hormone-binding protein (JHPB) family of proteins consists of several insect specific haemolymph juvenile hormone binding proteins. Juvenile hormone (JH) has a profound effect on insects. It regulates embryogenesis, maintains the status quo of larva development and stimulates reproductive maturation in the adult forms. JH is transported from the sites of its synthesis to target tissues by a haemolymph carrier called juvenile hormone-binding protein (JHBP). | https://en.wikipedia.org/wiki/Haemolymph_juvenile_hormone-binding_protein |
JHBP protects the JH molecules from hydrolysis by non-specific esterases present in the insect haemolymph. The crystal structure of the JHBP from Galleria mellonella (greater wax moth) shows an unusual fold consisting of a long alpha-helix wrapped in a much curved antiparallel beta-sheet. | https://en.wikipedia.org/wiki/Haemolymph_juvenile_hormone-binding_protein |
The folding pattern for this structure closely resembles that found in some tandem-repeat mammalian lipid-binding and bactericidal permeability-increasing proteins, with a similar organisation of the major cavity and a disulfide bond linking the long helix and the beta-sheet. It would appear that JHBP forms two cavities, only one of which, the one near the N- and C-termini, binds the hormone; binding induces a conformational change, of unknown significance. == References == | https://en.wikipedia.org/wiki/Haemolymph_juvenile_hormone-binding_protein |
In molecular biology, the haemolysin expression modulating protein family is a family of proteins. This family consists of haemolysin expression modulating protein (Hha) from Escherichia coli and its enterobacterial homologues, such as YmoA from Yersinia enterocolitica, and RmoA encoded on the R100 plasmid. These proteins act as modulators of bacterial gene expression. Members of this family act in conjunction with members of the H-NS family, participating in the thermoregulation of different virulence factors and in plasmid transfer. | https://en.wikipedia.org/wiki/Haemolysin_expression_modulating_protein_family |
Hha, along with the chromatin-associated protein H-NS, is involved in the regulation of expression of the toxin alpha-haemolysin in response to osmolarity and temperature. YmoA modulates the expression of various virulence factors, such as Yop proteins and YadA adhesin, in response to temperature. | https://en.wikipedia.org/wiki/Haemolysin_expression_modulating_protein_family |
RmoA is a plasmid R100 modulator involved in plasmid transfer. The HHA family of proteins display striking similarity to the oligomerisation domain of the H-NS proteins. == References == | https://en.wikipedia.org/wiki/Haemolysin_expression_modulating_protein_family |
In molecular biology, the heat-labile enterotoxin family includes Escherichia coli heat-labile enterotoxin (Elt or LT) and cholera toxin (Ctx) secreted by Vibrio cholerae. lt is so named because it is inactivated at high temperatures. | https://en.wikipedia.org/wiki/Heat-labile_enterotoxin |
In molecular biology, the hexon protein is a major coat protein found in adenoviruses. Hexon coat proteins are synthesised during late infection and form homo-trimers. The 240 copies of the hexon trimer that are produced are organised so that 12 lie on each of the 20 facets. The central 9 hexons in a facet are cemented together by 12 copies of polypeptide IX. | https://en.wikipedia.org/wiki/Hexon_protein |
The penton complex, formed by the peripentonal hexons and penton base (holding in place a fibre), lie at each of the 12 vertices. The hexon coat protein is a duplication consisting of two domains with a similar fold packed together like the nucleoplasmin subunits. Within a hexon trimer, the domains are arranged around a pseudo 6-fold axis. | https://en.wikipedia.org/wiki/Hexon_protein |
The domains have a beta-sandwich structure consisting of 8 strands in two sheets with a jelly-roll topology; each domain is heavily decorated with many insertions. Some hexon proteins contain a distinct C-terminal domain. | https://en.wikipedia.org/wiki/Hexon_protein |
Hexon directly recruits the cellular motor protein dynein in a pH-dependent manner. The dynein-regulatory protein, dynactin, was found to play a clear role in regulating the dynein-adenovirus complex transport to the nucleus. == References == | https://en.wikipedia.org/wiki/Hexon_protein |
In molecular biology, the hyccin protein family is a family of proteins which may have a role in the beta-catenin-Tcf/Lef signaling pathway, as well as in the process of myelination of the central and peripheral nervous system. One member of this family is hyccin, encoded by the FAM126A gene. Defects in Hyccin are the cause of Hypomyelination and Congenital Cataract (HCC), also called leukodystrophy hypomyelinating type 5 (HLD5). This disorder is characterised by congenital cataracts, progressive neurologic impairment, and diffuse myelin deficiency. Affected individuals experience progressive pyramidal and cerebellar dysfunction, muscle weakness and wasting prevailing in the lower limbs. | https://en.wikipedia.org/wiki/Hyccin_protein_family |
In molecular biology, the hydrogenase maturation protease family is a family of aspartic endopeptidases belonging to MEROPS family A31. The large subunit of -hydrogenase, as well as other nickel metalloenzymes, is synthesized as a precursor devoid of the metalloenzyme active site. This precursor undergoes a complex post-translational maturation process that requires a number of accessory proteins. | https://en.wikipedia.org/wiki/Hydrogenase_maturation_protease_family |
At one step of this process, after nickel incorporation, each hydrogenase isoenzyme is processed by proteolytic cleavage at the C-terminal end by the corresponding hydrogenase maturation endopeptidase. For example, Escherichia coli HycI is involved in processing of pre-HycE (the large subunit of hydrogenase 3),; HybD is involved in processing of pre-HybC (the large subunit of hydrogenase 2); and HyaD is assumed to be involved in processing of the large subunit of hydrogenase 1. The cleavage site is after a His or an Arg, liberating a short peptide. | https://en.wikipedia.org/wiki/Hydrogenase_maturation_protease_family |
This cleavage occurs only in the presence of nickel, and the endopeptidase probably uses the metal in the large subunit of -hydrogenases as a recognition motif. There is no direct evidence for the active site or substrate-binding site, but there are predictions based on an available structure.Nomenclature note: the following names are used in different organisms for members of this family: HycI, HybD, HyaD, HoxM, HoxW, HupD, HynC, HupM, VhoD, VhtD. Gene/protein names are sometimes used interchangeably to designate various "hydrogenase cluster" proteins unrelated to each other in various organisms. For example, the following names are used for members of this group, but also for unrelated proteins: HupD is used in Azotobacter chroococcum and Anabaena species to designate an unrelated hydrogenase maturation factor; HydD is used to designate hydrogenase structural genes in Thermococcus litoralis, Pyrococcus abyssi, and other species. | https://en.wikipedia.org/wiki/Hydrogenase_maturation_protease_family |
In molecular biology, the insect pheromone-binding family A10/OS-D is a family of small helical proteins postulated to contribute to the specificity of the insect’s olfactory system by binding components of the natural pheromone mixtures. A class of small (14-20 Kd) water-soluble proteins, called pheromone binding proteins, first discovered in the insect sensillar lymph but also found in the mucus of vertebrates, is postulated to mediate the solubilisation of hydrophobic odorant molecules, and thereby to facilitate their transport to the receptor neurons. The product of a gene expressed in the olfactory system of Drosophila melanogaster (Fruit fly), OS-D, shares features common to vertebrate odorant binding proteins, but has a primary structure unlike odorant-binding proteins. OS-D derivatives have subsequently been found in chemosensory organs of phylogenetically distinct insects, including cockroaches, phasmids and moths, suggesting that OS-D-like proteins seem to be conserved in the insect phylum. OS-D and related proteins are members of the insect pheromone-binding family A10/OS-D. | https://en.wikipedia.org/wiki/Insect_pheromone-binding_protein |
In molecular biology, the interferon gamma receptor (IFNGR1) family is a family of proteins which includes several eukaryotic and viral interferon gamma receptor proteins. Members of this family include: The human interferon gamma receptor 1, which is a member of the hematopoietic cytokine receptor superfamily. It is expressed in a membrane-bound form in many cell types, and is over-expressed in tumour cells. It comprises an extracellular portion of 229 amino acid residues, a single transmembrane region, and a cytoplasmic domain of 221 amino acid residues. | https://en.wikipedia.org/wiki/Interferon_gamma_receptor_(IFNGR1)_family |
As with other members of its superfamily, the cytokine-binding sites are formed by a small set of closely spaced surface loops that extend from a beta-sheet core, much like antigen-binding sites on antibodies. The vaccinia virus interferon (IFN)-gamma receptor (IFN-gammaR), which is a 43 kDa soluble glycoprotein that is secreted from infected cells early during infection. IFN-gammaR from vaccinia virus, cowpox virus and camelpox virus exist naturally as homodimers, whereas the cellular IFN-gammaR dimerises only upon binding the homodimeric IFN-gamma. The existence of the virus protein as a dimer in the absence of ligand may provide an advantage to the virus in efficient binding and inhibition of IFN-gamma in solution. == References == | https://en.wikipedia.org/wiki/Interferon_gamma_receptor_(IFNGR1)_family |
In molecular biology, the interferon-inducible GTPase (IIGP) family of proteins is thought to play a role in intracellular defence. IIGP is predominantly associated with the Golgi apparatus and also localises to the endoplasmic reticulum and exerts a distinct role in IFN-induced intracellular membrane trafficking or processing.Members of this family include interferon-inducible GTPase 5 and immunity-related GTPase family M protein. == References == | https://en.wikipedia.org/wiki/Interferon-inducible_GTPase |
In molecular biology, the iron dependent repressors are a family of bacterial and archaeal transcriptional repressors. At their N-terminus they contain a dtxR-type HTH domain. This is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 amino acids present in metalloregulators of the dtxR/mntR family. The domain is named after Corynebacterium diphtheriae dtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis mntR, a manganese transport regulator. | https://en.wikipedia.org/wiki/Iron_dependent_repressor |
Iron-responsive metalloregulators such as dtxR and ideR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like mntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea. The metalloregulators like dtxR/mntR contain the DNA-binding dtxR-type HTHdomain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. | https://en.wikipedia.org/wiki/Iron_dependent_repressor |
Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated mntR.Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The dtxR protein regulates the expression of diphtheria toxin in response to environmental iron concentrations. | https://en.wikipedia.org/wiki/Iron_dependent_repressor |
Furthermore, dtxR and ideR control iron uptake. Homeostasis of manganese, which is an essential nutrient, is regulated by mntR. A typical dtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. | https://en.wikipedia.org/wiki/Iron_dependent_repressor |
Iron-bound dtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three alpha-helices and a pair of antiparallel beta-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the beta-strands are called the wing. | https://en.wikipedia.org/wiki/Iron_dependent_repressor |
This wHTH topology is similar to the lysR-type HTH. Most dtxR-type metalloregulators bind as dimers to the DNA major groove. Several proteins are known to contain a dtxR-type HTH domain. | https://en.wikipedia.org/wiki/Iron_dependent_repressor |
These include: Corynebacterium diphtheriae dtxR, a diphtheria toxin repressor, which regulates the expression of the high-affinity iron uptake system, other iron-sensitive genes, and the bacteriophage tox gene. Metal-bound dtxR represses transcription by binding the tox operator; if iron is limiting, conformational changes of the wHTH disrupt DNA-binding and the diphtheria toxin is produced. Mycobacterium tuberculosis ideR, an iron-dependent regulator that is essential for this pathogen. | https://en.wikipedia.org/wiki/Iron_dependent_repressor |
The regulator represses genes for iron acquisition and activates iron storage genes, and is a positive regulator of oxidative stress responses. Bacillus subtilis mntR, a manganese transport regulator, binds Mn2+ as an effector and is a transcriptional repressor of transporters for the import of manganese. Treponema pallidum troR, a metal-dependent transcriptional repressor. Archaeoglobus fulgidus MDR1 (troR), a metal-dependent transcriptional repressor, which negatively regulates its own transcription. == References == | https://en.wikipedia.org/wiki/Iron_dependent_repressor |
In molecular biology, the iron response element or iron-responsive element (IRE) is a short conserved stem-loop which is bound by iron response proteins (IRPs, also named IRE-BP or IRBP). The IRE is found in UTRs (untranslated regions) of various mRNAs whose products are involved in iron metabolism. For example, the mRNA of ferritin (an iron storage protein) contains one IRE in its 5' UTR. When iron concentration is low, IRPs bind the IRE in the ferritin mRNA and cause reduced translation rates. In contrast, binding to multiple IREs in the 3' UTR of the transferrin receptor (involved in iron acquisition) leads to increased mRNA stability. | https://en.wikipedia.org/wiki/Iron_response_element |
In molecular biology, the isocitrate/isopropylmalate dehydrogenase family is a protein family consisting of the evolutionary related enzymes isocitrate dehydrogenase, 3-isopropylmalate dehydrogenase and tartrate dehydrogenase.Isocitrate dehydrogenase (IDH), is an important enzyme of carbohydrate metabolism which catalyses the oxidative decarboxylation of isocitrate into alpha-ketoglutarate. IDH is either dependent on NAD+ EC 1.1.1.41 or on NADP+ EC 1.1.1.42. In eukaryotes there are at least three isozymes of IDH: two are located in the mitochondrial matrix (one NAD+-dependent, the other NADP+-dependent), while the third one (also NADP+-dependent) is cytoplasmic. | https://en.wikipedia.org/wiki/Isocitrate/isopropylmalate_dehydrogenase_family |
In Escherichia coli the activity of a NADP+-dependent form of the enzyme is controlled by the phosphorylation of a serine residue; the phosphorylated form of IDH is completely inactivated. 3-isopropylmalate dehydrogenase EC 1.1.1.85 (IMDH) catalyses the third step in the biosynthesis of leucine in bacteria and fungi, the oxidative decarboxylation of 3-isopropylmalate into 2-oxo-4-methylvalerate.Tartrate dehydrogenase EC 1.1.1.93 catalyses the reduction of tartrate to oxaloglycolate. == References == | https://en.wikipedia.org/wiki/Isocitrate/isopropylmalate_dehydrogenase_family |
In molecular biology, the jacalin-like lectin domain is a mannose-binding lectin domain with a beta-prism fold consisting of three 4-stranded beta-sheets, with an internal pseudo 3-fold symmetry. Some lectins in this group stimulate distinct T- and B-cell functions, such as Jacalin, which binds to the T-antigen and acts as an agglutinin. This domain is found in 1 to 6 copies in lectins. The domain is also found in the salt-stress induced protein from rice and an animal prostatic spermine-binding protein. | https://en.wikipedia.org/wiki/Jacalin-like_lectin_domain |
Database of jacalin like lectins and structure function relations. Proteins containing this domain include: Jacalin, a tetrameric plant seed lectin and agglutinin from Artocarpus heterophyllus (jackfruit), which is specific for galactose. Artocarpin, a tetrameric plant seed lectin from A. heterophyllus. | https://en.wikipedia.org/wiki/Jacalin-like_lectin_domain |
Lectin MPA, a tetrameric plant seed lectin and agglutinin from Maclura pomifera (Osage orange). Heltuba lectin, a plant seed lectin and agglutinin from Helianthus tuberosus (Jerusalem artichoke). | https://en.wikipedia.org/wiki/Jacalin-like_lectin_domain |
Agglutinin from Calystegia sepium (Hedge bindweed). Griffithsin, an anti-viral lectin from red algae (Griffithsia species). == References == | https://en.wikipedia.org/wiki/Jacalin-like_lectin_domain |
In molecular biology, the killer toxin Kp4 family is a family of killer toxins, which includes the Kp4 killer toxin from the smut fungus Ustilago maydis.Killer toxins are polypeptides secreted by some fungal species ("killer yeasts") that kill sensitive cells of the same or related species, often functioning by creating pores in target cell membranes. The fungal killer toxin KP4 from the corn smut fungus, Ustilago maydis (Smut fungus), is encoded by a resident symbiotic double-stranded RNA virus, Ustilago maydis P4 virus (UmV4), within fungal cells. Unlike most killer toxins, KP4 is a single polypeptide. | https://en.wikipedia.org/wiki/Killer_toxin_Kp4_family |
KP4 inhibits voltage-gated calcium channels in mammalian cells, which in turn inhibits cell growth and division by blocking calcium import. KP4 adopts a structure consisting of a two-layer alpha/beta sandwich with a left-handed crossover. == References == | https://en.wikipedia.org/wiki/Killer_toxin_Kp4_family |
In molecular biology, the kinase binding protein CGI-121 family of proteins includes the kinase binding protein CGI-121 and its homologues. CGI-121 has been shown to bind to the p53-related protein kinase (PRPK). CGI-121 is part of a conserved protein complex, KEOPS. | https://en.wikipedia.org/wiki/Kinase_binding_protein_CGI-121 |
The KEOPS complex is involved in telomere uncapping and telomere elongation. This family of proteins also include archaeal homologues. == References == | https://en.wikipedia.org/wiki/Kinase_binding_protein_CGI-121 |
In molecular biology, the latexin family is a family of proteins which family consists of several animal specific latexin and proteins related to latexin that belong to MEROPS proteinase inhibitor family I47, clan IH.Latexin, a protein possessing inhibitory activity against rat carboxypeptidase A1 (CPA1) and CPA2 (MEROPS peptidase family M14A), is expressed in a neuronal subset in the cerebral cortex and cells in other neural and non-neural tissues of rat. OCX-32, the 32 kDa eggshell matrix protein, is present at high levels in the uterine fluid during the terminal phase of eggshell formation, and is localised predominantly in the outer eggshell. The timing of OCX-32 secretion into the uterine fluid suggests that it may play a role in the termination of mineral deposition. OCX-32 protein possesses limited identity (32%) to two unrelated proteins: latexin and to a skin protein that is encoded by a retinoic acid receptor-responsive gene, TIG1. | https://en.wikipedia.org/wiki/Latexin_family |
Tazarotene Induced Gene 1 (TIG1) is a putative transmembrane protein with a small N-terminal intracellular region, a single membrane-spanning hydrophobic region, and a large C-terminal extracellular region containing a glycosylation signal. TIG1 is up-regulated by retinoic acid receptor but not by retinoid X receptor-specific synthetic retinoids. TIG1 may be a tumour suppressor gene whose diminished expression is involved in the malignant progression of prostate cancer. == References == | https://en.wikipedia.org/wiki/Latexin_family |
In molecular biology, the leguminous lectin family is a family of lectin proteins. It is one of the largest lectin families with more than 70 lectins reported in a review in 1990. Leguminous lectins consist of two or four subunits, each containing one carbohydrate-binding site. The interaction with sugars requires tightly bound calcium and manganese ions. | https://en.wikipedia.org/wiki/Leguminous_lectin_family |
The structural similarities of these lectins are reported by the primary structural analyses and X-ray crystallographic studies. X-ray studies have shown that the folding of the polypeptide chains in the region of the carbohydrate-binding sites is also similar, despite differences in the primary sequences. The carbohydrate-binding sites of these lectins consist of two conserved amino acids on beta pleated sheets. | https://en.wikipedia.org/wiki/Leguminous_lectin_family |
One of these loops contains transition metals, calcium and manganese, which keep the amino acid residues of the sugar-binding site at the required positions. Amino acid sequences of this loop play an important role in the carbohydrate-binding specificities of these lectins. These lectins bind either glucose, mannose or galactose. | https://en.wikipedia.org/wiki/Leguminous_lectin_family |
The exact function of legume lectins is not known but they may be involved in the attachment of nitrogen-fixing bacteria to legumes and in the protection against pathogens.Some legume lectins are proteolytically processed to produce two chains, beta (which corresponds to the N-terminal) and alpha (C-terminal). The lectin concanavalin A (conA) from jack bean is exceptional in that the two chains are transposed and ligated (by formation of a new peptide bond). The N terminus of mature conA thus corresponds to that of the alpha chain and the C terminus to the beta chain. == References == | https://en.wikipedia.org/wiki/Leguminous_lectin_family |
In molecular biology, the linker histone H1 is a protein family forming a critical component of eukaryotic chromatin. H1 histones bind to the linker DNA exiting from the nucleosome core particle, while the core histones (H2A, H2B, H3 and H4) form the octamer core of the nucleosome around which the DNA is wrapped.H1 forms a complex family of related proteins with distinct specificity for tissues, developmental stages, and organisms in which they are expressed. Individual H1 proteins are often referred to as isoforms or variants. The discovery of H1 variants in calf thymus preceded the discovery of core histone variants. | https://en.wikipedia.org/wiki/Linker_histone_H1_variants |
In molecular biology, the lipid-binding serum glycoproteins family, also known as the BPI/LBP/Plunc family or LBP/BPI/CETP family represents a family which includes mammalian lipid-binding serum glycoproteins and/or proteins containing a structural motif known as the BPI fold. Members of this family include: Bactericidal permeability-increasing protein (BPI) Lipopolysaccharide-binding protein (LBP) Cholesteryl ester transfer protein (CETP) Phospholipid transfer protein (PLTP) Palate, lung and nasal epithelium carcinoma-associated protein (PLUNC) | https://en.wikipedia.org/wiki/Lipid-binding_serum_glycoprotein |
In molecular biology, the microRNA miR-219 was predicted in vertebrates by conservation between human, mouse and pufferfish and cloned in pufferfish. It was later predicted and confirmed experimentally in Drosophila. Homologs of miR-219 have since been predicted or experimentally confirmed in a wide range of species, including the platyhelminth Schmidtea mediterranea, several arthropod species and a wide range of vertebrates (MIPF0000044). | https://en.wikipedia.org/wiki/Mir-219_microRNA_precursor_family |
The hairpin precursors (represented here) are predicted based on base pairing and cross-species conservation; their extents are not known. In this case, the mature sequence is excised from the 5' arm of the hairpin. miR-219 has also been linked with NMDA receptor signalling in humans by targeting CaMKIIγ (a kind of protein kinase dependent to calcium and calmodulin) expression. And it has been suggested that deregulation of this miRNA can lead to the expression of mental disorders such as schizophrenia. Recent findings show that miR-219 is linked with Tau toxicity, suggesting that miR-219 is involved in neurodegenerative disease, such as Alzheimer's disease, Parkinson's disease etc. | https://en.wikipedia.org/wiki/Mir-219_microRNA_precursor_family |
In molecular biology, the myogenic determination factor 5 proteins are a family of proteins found in eukaryotes. This family includes the Myf5 protein, which is responsible for directing cells to the skeletal myocyte lineage during development. Myf5 is likely to act in a similar way to the other MRF4 proteins such as MyoD which perform the same function. These are histone acetyltransferases and histone deacetylases which activate and repress genes involved in the myocyte lineage. | https://en.wikipedia.org/wiki/Myogenic_determination_factor_5 |
Myogenic determination factor 5 proteins contain three conserved protein domains. A C-terminal Myf5 domain, a central basic helix-loop-helix (bHLH) domain and an N-terminal basic domain. The bHLH region mediates specific DNA binding. | https://en.wikipedia.org/wiki/Myogenic_determination_factor_5 |
With 12 residues of the basic domain involved in DNA binding. The basic domain forms an extended alpha helix in the structure. == References == | https://en.wikipedia.org/wiki/Myogenic_determination_factor_5 |
In molecular biology, the octopine dehydrogenase family of enzymes act on the CH-NH substrate bond using NAD(+) or NADP(+) as an acceptor. The family includes octopine dehydrogenase EC 1.5.1.11, nopaline dehydrogenase EC 1.5.1.19, lysopine dehydrogenase EC 1.5.1.16 and opine dehydrogenase EC 1.5.1.-. NADPH is the preferred cofactor, but NADH is also used. Octopine dehydrogenase is involved in the reductive condensation of arginine and pyruvic acid to D-octopine.Opine dehydrogenases can be found in both bacteria and marine cephalopods. | https://en.wikipedia.org/wiki/Octopine_dehydrogenase_family |
In bacteria, some of these opine dehydrogenases are involved in crown gall tumours that are produced by Agrobacterium spp., and which encode for the opine dehydrogenases on a Ti-plasmid. These bacteria can transfer a portion of this plasmid (T-DNA) to a susceptible plant cell; the T-DNA then integrates into the plant nuclear genome, where its genes can be expressed. Some of these genes direct the synthesis and secretion of unusual amino acid and sugar derivatives called opines - these opines are used as a carbon and sometimes a nitrogen source by the infecting bacteria. | https://en.wikipedia.org/wiki/Octopine_dehydrogenase_family |
Opine dehydrogenases are also found in the marine invertebrate cephalopods (octopuses, squid, and cuttlefish). For example, in marine cephalopods, octopine dehydrogenase activity in mantle muscle is significantly correlated with a species' ability to buffer the acidic end products of anaerobic metabolism, with activity declining strongly with a species' habitat depth. == References == | https://en.wikipedia.org/wiki/Octopine_dehydrogenase_family |
In molecular biology, the plant calmodulin-binding domain is a protein domain found repeated in a number of plant calmodulin-binding proteins. These domains are thought to constitute the calmodulin-binding domains of these proteins. Binding of the proteins to calmodulin depends on the presence of calcium ions. These proteins are thought to be involved in various processes, such as plant defence responses and stolonisation or tuberization. == References == | https://en.wikipedia.org/wiki/Plant_calmodulin-binding_domain |
In molecular biology, the polyketide synthesis cyclase family of proteins includes a number of cyclases involved in polyketide synthesis in a number of actinobacterial species. Aromatic polyketides are assembled by a type II (iterative) polyketide synthase in bacteria. Iterative type II polyketide syntheses produce polyketide chains of variable but defined length from a specific starter unit and a number of extender units. They also specify the initial regiospecific folding and cyclisation pattern of nascent polyketides either through the action of a cyclase (CYC) subunit or through the combined action of site-specific ketoreductase and CYC subunits. | https://en.wikipedia.org/wiki/Polyketide_synthesis_cyclase_family |
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