cd01653

Type 1 glutamine amidotransferase (GATase1)-like domain

CDD entry
Member databaseCDD
CDD typedomain
Short nameGATase1
SetGAT_1

Description

Type 1 glutamine amidotransferase (GATase1)-like domain. This group includes proteins similar to Class I glutamine amidotransferases, the intracellular PH1704 from Pyrococcus horikoshii, the C-terminal of the large catalase: Escherichia coli HP-II, Sinorhizobium meliloti Rm1021 ThuA. and, the A4 beta-galactosidase middle domain. The majority of proteins in this group have a reactive Cys found in the sharp turn between a beta strand and an alpha helix termed the nucleophile elbow. For Class I glutamine amidotransferases proteins which transfer ammonia from the amide side chain of glutamine to an acceptor substrate, this Cys forms a Cys-His-Glu catalytic triad in the active site. Glutamine amidotransferases activity can be found in a range of biosynthetic enzymes included in this cd: glutamine amidotransferase, formylglycinamide ribonucleotide, GMP synthetase, anthranilate synthase component II, glutamine-dependent carbamoyl phosphate synthase, cytidine triphosphate synthetase, gamma-glutamyl hydrolase, imidazole glycerol phosphate synthase and, cobyric acid synthase. For Pyrococcus horikoshii PH1704, the Cys of the nucleophile elbow together with a different His and, a Glu from an adjacent monomer form a catalytic triad different from the typical GATase1 triad. The E. coli HP-II C-terminal domain, S. meliloti Rm1021 ThuA and the A4 beta-galactosidase middle domain lack the catalytic triad typical GATaseI domains. GATase1-like domains can occur either as single polypeptides, as in Class I glutamine amidotransferases, or as domains in a much larger multifunctional synthase protein, such as CPSase.
[44, 9, 1, 59, 2, 5, 48, 28, 4, 49, 15, 14, 37, 20, 35, 41, 32, 50, 27, 52, 12, 58, 19, 30, 57, 18, 38, 47, 56, 25, 3, 42, 34, 7, 31, 24, 46, 8, 13, 43, 29, 6, 17, 55, 53, 45, 21, 10, 22, 11, 36, 16, 54, 60, 39, 33, 51, 40, 23, 26]

References

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2.The crystal structure of GMP synthetase reveals a novel catalytic triad and is a structural paradigm for two enzyme families. Tesmer JJ, Klem TJ, Deras ML, Davisson VJ, Smith JL. Nat. Struct. Biol. 3, 74-86, (1996). View articlePMID: 8548458

3.Substrate flow in catalases deduced from the crystal structures of active site variants of HPII from Escherichia coli. Melik-Adamyan W, Bravo J, Carpena X, Switala J, Mate MJ, Fita I, Loewen PC. Proteins 44, 270-81, (2001). View articlePMID: 11455600

4.The structures of anthranilate synthase of Serratia marcescens crystallized in the presence of (i) its substrates, chorismate and glutamine, and a product, glutamate, and (ii) its end-product inhibitor, L-tryptophan. Spraggon G, Kim C, Nguyen-Huu X, Yee MC, Yanofsky C, Mills SE. Proc. Natl. Acad. Sci. U.S.A. 98, 6021-6, (2001). View articlePMID: 11371633

5.Localization of two functions of the phosphoribosyl anthranilate transferase of Escherichia coli to distinct regions of the polypeptide chain. Jackson EN, Yanofsky C. J Bacteriol 117, 502-8, (1974). PMID: 4590474

6.The Parkinson's disease protein DJ-1 is neuroprotective due to cysteine-sulfinic acid-driven mitochondrial localization. Canet-Aviles RM, Wilson MA, Miller DW, Ahmad R, McLendon C, Bandyopadhyay S, Baptista MJ, Ringe D, Petsko GA, Cookson MR. Proc. Natl. Acad. Sci. U.S.A. 101, 9103-8, (2004). View articlePMID: 15181200

7.Crystal structure of the YDR533c S. cerevisiae protein, a class II member of the Hsp31 family. Graille M, Quevillon-Cheruel S, Leulliot N, Zhou CZ, de la Sierra Gallay IL, Jacquamet L, Ferrer JL, Liger D, Poupon A, Janin J, van Tilbeurgh H. Structure 12, 839-47, (2004). View articlePMID: 15130476

8.Crystal structure of an intracellular protease from Pyrococcus horikoshii at 2-A resolution. Du X, Choi IG, Kim R, Wang W, Jancarik J, Yokota H, Kim SH. Proc. Natl. Acad. Sci. U.S.A. 97, 14079-84, (2000). View articlePMID: 11114201

9.Enzymes with molecular tunnels. Raushel FM, Thoden JB, Holden HM. Acc. Chem. Res. 36, 539-48, (2003). View articlePMID: 12859215

10.Molecular characterization and regulation of an operon encoding a system for transport of arginine and ornithine and the ArgR regulatory protein in Pseudomonas aeruginosa. Nishijyo T, Park SM, Lu CD, Itoh Y, Abdelal AT. J Bacteriol 180, 5559-66, (1998). PMID: 9791103

11.AraC-XylS database: a family of positive transcriptional regulators in bacteria. Tobes R, Ramos JL. Nucleic Acids Res 30, 318-21, (2002). PMID: 11752325

12.The synthetase domains of cobalamin biosynthesis amidotransferases cobB and cobQ belong to a new family of ATP-dependent amidoligases, related to dethiobiotin synthetase. Galperin MY, Grishin NV. Proteins 41, 238-47, (2000). View articlePMID: 10966576

13.Crystal structure of catalase HPII from Escherichia coli. Bravo J, Verdaguer N, Tormo J, Betzel C, Switala J, Loewen PC, Fita I. Structure 3, 491-502, (1995). View articlePMID: 7663946

14.Structure of carbamoyl phosphate synthetase: a journey of 96 A from substrate to product. Thoden JB, Holden HM, Wesenberg G, Raushel FM, Rayment I. Biochemistry 36, 6305-16, (1997). View articlePMID: 9174345

15.Perforation of the tunnel wall in carbamoyl phosphate synthetase derails the passage of ammonia between sequential active sites. Kim J, Raushel FM. Biochemistry 43, 5334-40, (2004). View articlePMID: 15122899

16.A new native EcHsp31 structure suggests a key role of structural flexibility for chaperone function. Quigley PM, Korotkov K, Baneyx F, Hol WG. Protein Sci. 13, 269-77, (2004). View articlePMID: 14691241

17.Crystal structure of DJ-1/RS and implication on familial Parkinson's disease. Huai Q, Sun Y, Wang H, Chin LS, Li L, Robinson H, Ke H. FEBS Lett. 549, 171-5, (2003). View articlePMID: 12914946

18.Folate synthesis in plants: the p-aminobenzoate branch is initiated by a bifunctional PabA-PabB protein that is targeted to plastids. Basset GJ, Quinlivan EP, Ravanel S, Rebeille F, Nichols BP, Shinozaki K, Seki M, Adams-Phillips LC, Giovannoni JJ, Gregory JF 3rd, Hanson AD. Proc Natl Acad Sci U S A 101, 1496-501, (2004). PMID: 14745019

19.The C-terminal domain of HPII catalase is a member of the type I glutamine amidotransferase superfamily. Horvath MM, Grishin NV. Proteins 42, 230-6, (2001). View articlePMID: 11119647

20.The small subunit of carbamoyl phosphate synthetase: snapshots along the reaction pathway. Thoden JB, Huang X, Raushel FM, Holden HM. Biochemistry 38, 16158-66, (1999). View articlePMID: 10587438

21.Cloning and characterization of argR, a gene that participates in regulation of arginine biosynthesis and catabolism in Pseudomonas aeruginosa PAO1. Park SM, Lu CD, Abdelal AT. J Bacteriol 179, 5300-8, (1997). PMID: 9286980

22.Growing repertoire of AraC/XylS activators. Egan SM. J Bacteriol 184, 5529-32, (2002). PMID: 12270809

23.The gene encoding the biotin-apoprotein ligase of Saccharomyces cerevisiae. Cronan JE Jr, Wallace JC. FEMS Microbiol. Lett. 130, 221-9, (1995). View articlePMID: 7649444

24.Evolution of aminobenzoate synthases: nucleotide sequences of Salmonella typhimurium and Klebsiella aerogenes pabB. Goncharoff P, Nichols BP. Mol Biol Evol 5, 531-48, (1988). PMID: 3057324

25.Regulation and oxidation of two large monofunctional catalases. Michan S, Lledias F, Baldwin JD, Natvig DO, Hansberg W. Free Radic Biol Med 33, 521-32, (2002). PMID: 12160934

26.Yeast mutants defective in acetyl-coenzyme A carboxylase and biotin: apocarboxylase ligase. Mishina M, Roggenkamp R, Schweizer E. Eur J Biochem 111, 79-87, (1980). PMID: 6108218

27.Substrate-induced changes in the ammonia channel for imidazole glycerol phosphate synthase. Myers RS, Jensen JR, Deras IL, Smith JL, Davisson VJ. Biochemistry 42, 7013-22, (2003). View articlePMID: 12795596

28.The crystal structure of anthranilate synthase from Sulfolobus solfataricus: functional implications. Knochel T, Ivens A, Hester G, Gonzalez A, Bauerle R, Wilmanns M, Kirschner K, Jansonius JN. Proc. Natl. Acad. Sci. U.S.A. 96, 9479-84, (1999). View articlePMID: 10449718

29.Crystal structures of human DJ-1 and Escherichia coli Hsp31, which share an evolutionarily conserved domain. Lee SJ, Kim SJ, Kim IK, Ko J, Jeong CS, Kim GH, Park C, Kang SO, Suh PG, Lee HS, Cha SS. J. Biol. Chem. 278, 44552-9, (2003). View articlePMID: 12939276

30.Evolutionary and functional relationships within the DJ1 superfamily. Bandyopadhyay S, Cookson MR. BMC Evol. Biol. 4, 6, (2004). View articlePMID: 15070401

31.The 1.8-A resolution crystal structure of YDR533Cp from Saccharomyces cerevisiae: a member of the DJ-1/ThiJ/PfpI superfamily. Wilson MA, St Amour CV, Collins JL, Ringe D, Petsko GA. Proc. Natl. Acad. Sci. U.S.A. 101, 1531-6, (2004). View articlePMID: 14745011

32.Three-dimensional structure of human gamma -glutamyl hydrolase. A class I glatamine amidotransferase adapted for a complex substate. Li H, Ryan TJ, Chave KJ, Van Roey P. J. Biol. Chem. 277, 24522-9, (2002). View articlePMID: 11953431

33.Role of trehalose transport and utilization in Sinorhizobium meliloti--alfalfa interactions. Jensen JB, Ampomah OY, Darrah R, Peters NK, Bhuvaneswari TV. Mol. Plant Microbe Interact. 18, 694-702, (2005). View articlePMID: 16042015

34.Transcriptional analysis of the Azospirillum brasilense indole-3-pyruvate decarboxylase gene and identification of a cis-acting sequence involved in auxin responsive expression. Vande Broek A, Gysegom P, Ona O, Hendrickx N, Prinsen E, Van Impe J, Vanderleyden J. Mol Plant Microbe Interact 18, 311-23, (2005). PMID: 15828683

35.Crystal structure of Escherichia coli cytidine triphosphate synthetase, a nucleotide-regulated glutamine amidotransferase/ATP-dependent amidoligase fusion protein and homologue of anticancer and antiparasitic drug targets. Endrizzi JA, Kim H, Anderson PM, Baldwin EP. Biochemistry 43, 6447-63, (2004). View articlePMID: 15157079

36.The AraC transcriptional activators. Martin RG, Rosner JL. Curr Opin Microbiol 4, 132-7, (2001). PMID: 11282467

37.Carbamoyl phosphate synthetase: caught in the act of glutamine hydrolysis. Thoden JB, Miran SG, Phillips JC, Howard AJ, Raushel FM, Holden HM. Biochemistry 37, 8825-31, (1998). View articlePMID: 9636022

38.Probing the active site of homoserine trans-succinylase. Rosen R, Becher D, Buttner K, Biran D, Hecker M, Ron EZ. FEBS Lett. 577, 386-92, (2004). View articlePMID: 15556615

39.Trimeric crystal structure of the glycoside hydrolase family 42 beta-galactosidase from Thermus thermophilus A4 and the structure of its complex with galactose. Hidaka M, Fushinobu S, Ohtsu N, Motoshima H, Matsuzawa H, Shoun H, Wakagi T. J. Mol. Biol. 322, 79-91, (2002). View articlePMID: 12215416

40.Pleiotropic phenotype of acetyl-CoA-carboxylase-defective yeast cells--viability of a BPL1-amber mutation depending on its readthrough by normal tRNA(Gln)(CAG). Hoja U, Wellein C, Greiner E, Schweizer E. Eur J Biochem 254, 520-6, (1998). PMID: 9688262

41.Linkage of genes encoding enolase (eno) and CTP synthase (pyrG) in the beta-subdivision proteobacterium Nitrosomonas europaea. Mahony TJ, Miller DJ. FEMS Microbiol. Lett. 165, 153-7, (1998). PMID: 9711852

42.A novel zebrafish gene expressed specifically in the photoreceptor cells of the retina. Chang H, Gilbert W. Biochem Biophys Res Commun 237, 84-9, (1997). PMID: 9266834

43.The 1.1-A resolution crystal structure of DJ-1, the protein mutated in autosomal recessive early onset Parkinson's disease. Wilson MA, Collins JL, Hod Y, Ringe D, Petsko GA. Proc. Natl. Acad. Sci. U.S.A. 100, 9256-61, (2003). View articlePMID: 12855764

44.The amidotransferase family of enzymes: molecular machines for the production and delivery of ammonia. Raushel FM, Thoden JB, Holden HM. Biochemistry 38, 7891-9, (1999). View articlePMID: 10387030

45.Proper SUMO-1 conjugation is essential to DJ-1 to exert its full activities. Shinbo Y, Niki T, Taira T, Ooe H, Takahashi-Niki K, Maita C, Seino C, Iguchi-Ariga SM, Ariga H. Cell Death Differ. 13, 96-108, (2006). View articlePMID: 15976810

46.Sequence, expression in Escherichia coli, and analysis of the gene encoding a novel intracellular protease (PfpI) from the hyperthermophilic archaeon Pyrococcus furiosus. Halio SB, Blumentals II, Short SA, Merrill BM, Kelly RM. J. Bacteriol. 178, 2605-12, (1996). View articlePMID: 8626329

47.Enzyme-catalyzed acylation of homoserine: mechanistic characterization of the Escherichia coli metA-encoded homoserine transsuccinylase. Born TL, Blanchard JS. Biochemistry 38, 14416-23, (1999). View articlePMID: 10572016

48.Immunological study of anthranilate synthetase. Reiners JJ Jr, Zalkin H. J Bacteriol 123, 620-30, (1975). PMID: 50316

49.Structure of the cooperative allosteric anthranilate synthase from Salmonella typhimurium. Morollo AA, Eck MJ. Nat. Struct. Biol. 8, 243-7, (2001). View articlePMID: 11224570

50.Toward understanding the mechanism of the complex cyclization reaction catalyzed by imidazole glycerolphosphate synthase: crystal structures of a ternary complex and the free enzyme. Chaudhuri BN, Lange SC, Myers RS, Davisson VJ, Smith JL. Biochemistry 42, 7003-12, (2003). View articlePMID: 12795595

51.Redundancy in periplasmic binding protein-dependent transport systems for trehalose, sucrose, and maltose in Sinorhizobium meliloti. Jensen JB, Peters NK, Bhuvaneswari TV. J. Bacteriol. 184, 2978-86, (2002). View articlePMID: 12003938

52.Three-dimensional structure of YaaE from Bacillus subtilis, a glutaminase implicated in pyridoxal-5'-phosphate biosynthesis. Bauer JA, Bennett EM, Begley TP, Ealick SE. J. Biol. Chem. 279, 2704-11, (2004). View articlePMID: 14585832

53.DJ-1 up-regulates glutathione synthesis during oxidative stress and inhibits A53T alpha-synuclein toxicity. Zhou W, Freed CR. J Biol Chem 280, 43150-8, (2005). PMID: 16227205

54.The 1.6-A crystal structure of the class of chaperones represented by Escherichia coli Hsp31 reveals a putative catalytic triad. Quigley PM, Korotkov K, Baneyx F, Hol WG. Proc. Natl. Acad. Sci. U.S.A. 100, 3137-42, (2003). View articlePMID: 12621151

55.Drosophila DJ-1 mutants show oxidative stress-sensitive locomotive dysfunction. Park J, Kim SY, Cha GH, Lee SB, Kim S, Chung J. Gene 361, 133-9, (2005). PMID: 16203113

56.Structure of catalase HPII from Escherichia coli at 1.9 A resolution. Bravo J, Mate MJ, Schneider T, Switala J, Wilson K, Loewen PC, Fita I. Proteins 34, 155-66, (1999). PMID: 10022351

57.Para-aminobenzoate synthase gene of Saccharomyces cerevisiae encodes a bifunctional enzyme. Edman JC, Goldstein AL, Erbe JG. Yeast 9, 669-75, (1993). PMID: 8346682

58.Purification and characterization of cobyrinic acid a,c-diamide synthase from Pseudomonas denitrificans. Debussche L, Thibaut D, Cameron B, Crouzet J, Blanche F. J. Bacteriol. 172, 6239-44, (1990). View articlePMID: 2172209

59.Domain organization of Salmonella typhimurium formylglycinamide ribonucleotide amidotransferase revealed by X-ray crystallography. Anand R, Hoskins AA, Stubbe J, Ealick SE. Biochemistry 43, 10328-42, (2004). View articlePMID: 15301531

60.The crystal structure of Escherichia coli heat shock protein YedU reveals three potential catalytic active sites. Zhao Y, Liu D, Kaluarachchi WD, Bellamy HD, White MA, Fox RO. Protein Sci. 12, 2303-11, (2003). View articlePMID: 14500888

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