Protein Family Models

3',5'-cyclic nucleotide phosphodiesterase catalyzes the hydrolysis of cAMP or cGMP to produce adenosine 5'-phosphate or guanosine 5'-phosphate, respectively

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2024-02-09

guanosine monophosphate kinase (GMPK), also known as guanylate kinase (GKase)

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2024-02-09

3',5'-cyclic nucleotide phosphodiesterase catalyzes the hydrolysis of cAMP or cGMP to produce adenosine 5'-phosphate or guanosine 5'-phosphate, respectively

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2024-02-09

3',5'-cyclic nucleotide phosphodiesterase catalyzes the hydrolysis of cAMP or cGMP to produce adenosine 5'-phosphate or guanosine 5'-phosphate, respectively

Date:

2024-02-09

3',5'-cyclic nucleotide phosphodiesterase catalyzes the hydrolysis of cAMP or cGMP to produce adenosine 5'-phosphate or guanosine 5'-phosphate, respectively

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2024-02-09

bifunctional (p)ppGpp synthetase/guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase mediates the stringent response by producing and regulating the metabolism of the intracellular signaling alarmone (p)ppGpp

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2024-02-09

RhoGAP-FF1 is the FF domain of the Rho GTPase activating proteins (GAPs). These are the key proteins that make the switch between the active guanosine-triphosphate-bound form of Rho guanosine triphosphatases (GTPases) and the inactive guanosine-diphosphate-bound form. Rho guanosine triphosphatases (GTPases) are a family of proteins with key roles in the regulation of actin cytoskeleton dynamics. The RhoGAP-FF1 region contains the FF domain that has been implicated in binding to the transcription factor TFII-I; and phosphorylation of Tyr308 within the first FF domain inhibits this interaction. The RhoGAPFF1 domain constitutes the first solved structure of an FF domain that lacks the first of the two highly conserved Phe residues, but the substitution of Phe by Tyr does not affect the domain fold [1]. [1]. 19393245. NMR structural studies on human p190-A RhoGAPFF1 revealed that. domain phosphorylation by the PDGF-receptor alpha requires its. previous unfolding.. Bonet R, Ruiz L, Aragon E, Martin-Malpartida P, Macias MJ;. J Mol Biol. 2009;389:230-237. (from Pfam)

Date:

2024-08-14

Rhodopsin is the archetypal G-protein-coupled receptor. Such receptors participate in virtually all physiological processes, as signalling molecules. They utilise heterotrimeric guanosine triphosphate (GTP)-binding proteins to transduce extracellular signals to intracellular events. Rhodopsin is important because of the pivotal role it plays in visual signal transduction. Rhodopsin is a dimeric transmembrane protein and its intradiskal surface consists of this amino terminal domain and three loops connecting six of the seven transmembrane helices. The N-terminus is a compact domain of alpha-helical regions with breaks and bends at proline residues outside the membrane [1]. The transmembrane part of rhodopsin is represented by 7tm_1 (Pfam:PF00001). The N-terminal domain is extracellular is and is necessary for successful dimerisation and molecular stability [2]. [1]. 10888202. Structures of the intradiskal loops and amino terminus of the. G-protein receptor, rhodopsin.. Yeagle PL, Salloum A, Chopra A, Bhawsar N, Ali L, Kuzmanovski G,. Alderfer JL, Albert AD;. J Pept Res. 2000;55:455-465.. [2]. 16567090. Structure of the rhodopsin dimer: a working model for. G-protein-coupled receptors.. Fotiadis D, Jastrzebska B, Philippsen A, Muller DJ, Palczewski. K, Engel A;. Curr Opin Struct Biol. 2006;16:252-259. (from Pfam)

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2024-08-14

Members of this family of proteins catalyse the conversion of guanosine triphosphate (GTP) to 3',5'-cyclic guanosine monophosphate (cGMP) and pyrophosphate. (from Pfam)

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2024-08-14

These proteins share a region of similarity that falls towards the C terminus from Pfam:PF00575. [1]. 2649894. Yeast translation initiation suppressor sui2 encodes the alpha. subunit of eukaryotic initiation factor 2 and shares sequence. identity with the human alpha subunit.. Cigan AM, Pabich EK, Feng L, Donahue TF;. Proc Natl Acad Sci U S A 1989;86:2784-2788.. [2]. 14607111. The crystal structure of the N-terminal region of the alpha. subunit of translation initiation factor 2 (eIF2alpha) from. Saccharomyces cerevisiae provides a view of the loop containing. serine 51, the target of the eIF2alpha-specific kinases.. Dhaliwal S, Hoffman DW;. J Mol Biol 2003;334:187-195.. [3]. 14532131. The roles of initiation factor 2 and guanosine triphosphate in. initiation of protein synthesis.. Antoun A, Pavlov MY, Andersson K, Tenson T, Ehrenberg M;. EMBO J 2003;22:5593-5601.. [4]. 12762044. Universal translation initiation factor IF2/eIF5B.. Dever TE, Roll-Mecak A, Choi SK, Lee JH, Cao C, Shin BS, Burley. SK;. Cold Spring Harb Symp Quant Biol 2001;66:417-424. (from Pfam)

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2024-08-14

This family of proteins participate in the biosynthesis of 7-carboxy-7-deazaguanine. They catalyse the conversion of 7-deaza-7-carboxyguanine to preQ0 [1-3]. [1]. 14660578. Identification of four genes necessary for biosynthesis of the. modified nucleoside queuosine.. Reader JS, Metzgar D, Schimmel P, de Crecy-Lagard V;. J Biol Chem. 2004;279:6280-6285.. [2]. 16199558. Genetic analysis identifies a function for the queC (ybaX) gene. product at an initial step in the queuosine biosynthetic pathway. in Escherichia coli.. Gaur R, Varshney U;. J Bacteriol. 2005;187:6893-6901.. [3]. 19354300. The deazapurine biosynthetic pathway revealed: in vitro. enzymatic synthesis of PreQ(0) from guanosine 5'-triphosphate in. four steps.. McCarty RM, Somogyi A, Lin G, Jacobsen NE, Bandarian V;. Biochemistry. 2009;48:3847-3852.. [4]. 18491386. Crystal structure of QueC from Bacillus subtilis: an enzyme. involved in preQ1 biosynthesis.. Cicmil N, Huang RH;. Proteins. 2008;72:1084-1088. (from Pfam)

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2024-08-14

Retinal rod and cone cGMP phosphodiesterases function as the effector enzymes in the vertebrate visual transduction cascade. This family represents the inhibitory gamma subunit [1], which is also expressed outside retinal tissues and has been shown to interact with the G-protein-coupled receptor kinase 2 signalling system to regulate the epidermal growth factor- and thrombin-dependent stimulation of p42/p44 mitogen-activated protein kinase in human embryonic kidney 293 cells [2]. [1]. 11900530. Direct interaction of the inhibitory gamma-subunit of Rod cGMP. phosphodiesterase (PDE6) with the PDE6 GAFa domains.. Muradov KG, Granovsky AE, Schey KL, Artemyev NO;. Biochemistry 2002;41:3884-3890.. [2]. 11502744. The inhibitory gamma subunit of the type 6 retinal cyclic. guanosine monophosphate phosphodiesterase is a novel. intermediate regulating p42/p44 mitogen-activated protein kinase. signaling in human embryonic kidney 293 cells.. Wan KF, Sambi BS, Frame M, Tate R, Pyne NJ;. J Biol Chem 2001;276:37802-37808. (from Pfam)

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2024-08-14

This region of unknown function is found in RelA and SpoT of Escherichia coli, and their homologues in plants and in other eubacteria. RelA is a guanosine 3',5'-bis-pyrophosphate (ppGpp) synthetase (EC:2.7.6.5) while SpoT is thought to be a bifunctional enzyme catalysing both ppGpp synthesis and degradation (ppGpp 3'-pyrophosphohydrolase, (EC:3.1.7.2)) [1]. This region is often found in association with HD (Pfam:PF01966), a metal-dependent phosphohydrolase, TGS (Pfam:PF02824) which is a possible nucleotide-binding region, and the ACT regulatory domain (Pfam:PF01842). [1]. 2005134. Residual guanosine 3',5'-bispyrophosphate synthetic activity of. relA null mutants can be eliminated by spoT null mutations.. Xiao H, Kalman M, Ikehara K, Zemel S, Glaser G, Cashel M;. J Biol Chem 1991;266:5980-5990. (from Pfam)

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2024-08-14

The UDP-glucose/GDP-mannose dehydrogenaseses are a small group of enzymes which possesses the ability to catalyse the NAD-dependent 2-fold oxidation of an alcohol to an acid without the release of an aldehyde intermediate [2]. [1]. 2470755. Purification and characterization of guanosine. diphospho-D-mannose dehydrogenase. A key enzyme in the. biosynthesis of alginate by Pseudomonas aeruginosa.. Roychoudhury S, May TB, Gill JF, Singh SK, Feingold DS,. Chakrabarty AM;. J Biol Chem 1989;264:9380-9385.. [2]. 9013585. Properties and kinetic analysis of UDP-glucose dehydrogenase. from group A streptococci. Irreversible inhibition by. UDP-chloroacetol.. Campbell RE, Sala RF, van de Rijn I, Tanner ME;. J Biol Chem 1997;272:3416-3422. (from Pfam)

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2024-08-14

The UDP-glucose/GDP-mannose dehydrogenaseses are a small group of enzymes which possesses the ability to catalyse the NAD-dependent 2-fold oxidation of an alcohol to an acid without the release of an aldehyde intermediate [2]. [1]. 2470755. Purification and characterization of guanosine. diphospho-D-mannose dehydrogenase. A key enzyme in the. biosynthesis of alginate by Pseudomonas aeruginosa.. Roychoudhury S, May TB, Gill JF, Singh SK, Feingold DS,. Chakrabarty AM;. J Biol Chem 1989;264:9380-9385.. [2]. 9013585. Properties and kinetic analysis of UDP-glucose dehydrogenase. from group A streptococci. Irreversible inhibition by. UDP-chloroacetol.. Campbell RE, Sala RF, van de Rijn I, Tanner ME;. J Biol Chem 1997;272:3416-3422. (from Pfam)

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2024-08-14

The TGS domain is named after ThrRS, GTPase, and SpoT [1]. Interestingly, TGS domain was detected also at the amino terminus of the uridine kinase from the spirochaete Treponema pallidum (but not any other organism, including the related spirochaete Borrelia burgdorferi). TGS is a small domain that consists of ~50 amino acid residues and is predicted to possess a predominantly beta-sheet structure. There is no direct information on the functions of the TGS domain, but its presence in two types of regulatory proteins (the GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, regulatory role [1]. [1]. 10447505. Evolution of aminoacyl-tRNA synthetases--analysis of unique. domain architectures and phylogenetic trees reveals a complex. history of horizontal gene transfer events.. Wolf YI, Aravind L, Grishin NV, Koonin EV;. Genome Res 1999;9:689-710.. [2]. 10319817. The structure of threonyl-tRNA synthetase-tRNA(Thr) complex. enlightens its repressor activity and reveals an essential zinc. ion in the active site.. Sankaranarayanan R, Dock-Bregeon AC, Romby P, Caillet J,. Springer M, Rees B, Ehresmann C, Ehresmann B, Moras D;. Cell 1999;97:371-381. (from Pfam)

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2024-08-14

The methyltransferase TYW3 (tRNA-yW- synthesising protein 3) has been identified in yeast to be involved in wybutosine (yW) biosynthesis [1]. yW is a complexly modified guanosine residue that contains a tricyclic base and is found at the 3' position adjacent the anticodon of phenylalanine tRNA. TYW3 is an N-4 methylase that methylates yW-86 to yield yW-72 in an Ado-Met-dependent manner [1]. [1]. 16642040. Biosynthesis of wybutosine, a hyper-modified nucleoside in. eukaryotic phenylalanine tRNA.. Noma A, Kirino Y, Ikeuchi Y, Suzuki T;. EMBO J. 2006; [Epub ahead of print] (from Pfam)

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2024-08-14

This family consists of the N-terminal region of exopolyphosphatase (Ppx) EC:3.6.1.11 and guanosine pentaphosphate phospho-hydrolase (GppA) EC:3.6.1.40. [1]. 8212131. Exopolyphosphate phosphatase and guanosine pentaphosphate. phosphatase belong to the sugar kinase/actin/hsp 70 superfamily.. Reizer J, Reizer A, Saier MH Jr, Bork P, Sander C;. Trends Biochem Sci 1993;18:247-248. (from Pfam)

Date:

2024-08-14

Double cache domain 1 covers the last three strands from the membrane distal PAS-like domain, the first two strands of the membrane proximal domain, and the connecting elements between the two domains [2]. This domain when present in chemoreceptors recognise several signals such as proteinogenic amino acids, GABA, Histamine and polyamines, decanoic acid, Autoinducer-2, purine derivatives, quaternary amines, citrate and taurine, among others. When associated with histidine kinases, it recognises C3/C4-dicarboxylic acids, Spermine, guanosine and Autoinducer-2 (Mantilla et al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1 https://doi.org/10.1093/femsre/fuab043). [1]. 11084361. Cache - a signaling domain common to animal Ca(2+)-channel. subunits and a class of prokaryotic chemotaxis receptors.. Anantharaman V, Aravind L;. Trends Biochem Sci 2000;25:535-537.. [2]. 27049771. Cache Domains That are Homologous to, but Different from PAS. Domains Comprise the Largest Superfamily of Extracellular. Sensors in Prokaryotes.. Upadhyay AA, Fleetwood AD, Adebali O, Finn RD, Zhulin IB;. PLoS Comput Biol. 2016;12:e1004862. (from Pfam)

Date:

2024-08-14

This entry represents mRNA (guanine-N(7))-methyltransferase, which can either be found as a single domain protein, or as a domain within the mRNA-capping enzyme catalytic subunit. mRNA (guanine-N(7))-methyltransferase methylates the N7 position of the added guanosine to the 5'-cap structure of mRNAs. It binds RNA containing 5'-terminal GpppC [1-5]. Viral mRNA capping enzymes, meanwhile, are multidomain proteins that catalyse the first two reactions in the mRNA cap formation pathway [5]. They are heterodimers consisting of a large (catalytic) and small subunit. [1]. 9275164. Phylogeny of mRNA capping enzymes.. Wang SP, Deng L, Ho CK, Shuman S;. Proc Natl Acad Sci U S A 1997;94:9573-9578.. [2]. 10679253. Cloning and characterization of mRNA capping enzyme and mRNA. (Guanine-7-)-methyltransferase cDNAs from Xenopus laevis.. Yokoska J, Tsukamoto T, Miura Ki, Shiokawa K, Mizumoto K;. Biochem Biophys Res Commun. 2000;268:617-624.. [3]. 9790902. Cloning and characterization of three human cDNAs encoding mRNA. (guanine-7-)-methyltransferase, an mRNA cap methylase.. Tsukamoto T, Shibagaki Y, Niikura Y, Mizumoto K;. Biochem Biophys Res Commun. 1998;251:27-34.. [4]. 27422871. Molecular basis of RNA guanine-7 methyltransferase (RNMT). activation by RAM.. Varshney D, Petit AP, Bueren-Calabuig JA, Jansen C, Fletcher DA,. Peggie M, Weidlich S, Scullion P, Pisliakov AV, Cowling VH;. Nucleic Acids Res. 2016;44:10423-10436.. [5]. 24607143. Crystal structure of vaccinia virus mRNA capping enzyme provides. insights into the mechanism and evolution of the capping. apparatus.. Kyrieleis OJ, Chang J, de la Pena M, Shuman S, Cusack S;. Structure.. TRUNCATED at 1650 bytes (from Pfam)

Date:

2024-08-14