EzCatDB: S00294

DB codeS00294
RLCP classification3.1144.1800.89
CATH domainDomain 13.40.50.170Catalytic domain
E.C.2.1.2.2
CSA1c2t,1cde,1grc

CATH domainRelated DB codes (homologues)
3.40.50.170D00087

Enzyme Name
Swiss-protKEGG

P08179
Protein namePhosphoribosylglycinamide formyltransferasephosphoribosylglycinamide formyltransferase
2-amino-N-ribosylacetamide 5'-phosphate transformylase
GAR formyltransferase
GAR transformylase
glycinamide ribonucleotide transformylase
GAR TFase
5,10-methenyltetrahydrofolate:2-amino-N-ribosylacetamideribonucleotide transformylase
SynonymsEC 2.1.2.2
5''-phosphoribosylglycinamide transformylase
GAR transformylase
GART

KEGG pathways
MAP codePathways
MAP00230Purine metabolism
MAP00670One carbon pool by folate

Swiss-prot:Accession NumberP08179
Entry namePUR3_ECOLI
Activity10-formyltetrahydrofolate + N(1)-(5-phospho-D- ribosyl)glycinamide = tetrahydrofolate + N(2)-formyl-N(1)-(5- phospho-D-ribosyl)glycinamide.
SubunitMonomer. Homodimer below pH 6.8.
Subcellular location
Cofactor


SubstratesProductsintermediates
KEGG-idC00234C03838C00101C04376
Compound10-Formyltetrahydrofolate5'-PhosphoribosylglycinamideTetrahydrofolate5'-Phosphoribosyl-N-formylglycinamide
Typeamino acids,amide group,amine group,aromatic ring (only carbon atom),aromatic ring (with nitrogen atoms),carboxyl groupamide group,amine group,carbohydrate,phosphate group/phosphate ionamino acids,amide group,amine group,aromatic ring (only carbon atom),aromatic ring (with nitrogen atoms),carboxyl groupamide group,amine group,carbohydrate,phosphate group/phosphate ion
1c2tAAnalogue:NHSBound:GARUnboundUnboundUnbound
1c2tBAnalogue:NHSBound:GARUnboundUnboundUnbound
1c3eAAnalogue:NHRBound:GARUnboundUnboundUnbound
1c3eBAnalogue:NHRBound:GARUnboundUnboundUnbound
1cddAUnboundUnboundUnboundUnboundUnbound
1cddBUnboundUnboundUnboundUnboundUnbound
1cdeAUnboundBound:GARAnalogue:DZFUnboundUnbound
1cdeBUnboundBound:GARAnalogue:DZFUnboundUnbound
1cdeCUnboundBound:GARAnalogue:DZFUnboundUnbound
1cdeDUnboundBound:GARAnalogue:DZFUnboundUnbound
1garAAnalogue:U89UnboundUnboundUnboundUnbound
1garBAnalogue:U89UnboundUnboundUnboundUnbound
1grcAUnboundUnboundUnboundUnboundUnbound
1grcBUnboundUnboundUnboundUnboundUnbound
1jkxAUnboundUnboundUnboundUnboundIntermediate-analogue:138
1jkxBUnboundUnboundUnboundUnboundIntermediate-analogue:138
1jkxCUnboundUnboundUnboundUnboundIntermediate-analogue:138
1jkxDUnboundUnboundUnboundUnboundIntermediate-analogue:138
2garAUnboundUnboundUnboundUnboundUnbound
3garAUnboundUnboundUnboundUnboundUnbound

Active-site residues
resource
literature [2]
pdbCatalytic residues
1c2tAASN 106;HIS 108;ASP 144
1c2tBASN 106;HIS 108;ASP 144
1c3eAASN 106;HIS 108;ASP 144
1c3eBASN 106;HIS 108;ASP 144
1cddAASN 106;HIS 108;ASP 144
1cddBASN 106;HIS 108;ASP 144
1cdeAASN 106;HIS 108;ASP 144
1cdeBASN 106;HIS 108;ASP 144
1cdeCASN 106;HIS 108;ASP 144
1cdeDASN 106;HIS 108;ASP 144
1garAASN 106;HIS 108;ASP 144
1garBASN 106;HIS 108;ASP 144
1grcAASN 106;HIS 108;ASP 144
1grcBASN 106;HIS 108;ASP 144
1jkxAASN 106;HIS 108;ASP 144
1jkxBASN 106;HIS 108;ASP 144
1jkxCASN 106;HIS 108;ASP 144
1jkxDASN 106;HIS 108;ASP 144
2garAASN 106;HIS 108;ASP 144
3garAASN 106;HIS 108;ASP 144

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[1]Fig.9, p.6686
[2]p.6118
[4]Fig.8, p.1673
[5]Fig.2
[12]Fig.7, Fig.83
[15]Fig.9, p.10029

references
[1]
PubMed ID2204419
JournalBiochemistry
Year1990
Volume29
Pages6678-87
AuthorsInglese J, Smith JM, Benkovic SJ
TitleActive-site mapping and site-specific mutagenesis of glycinamide ribonucleotide transformylase from Escherichia coli.
Related Swiss-protP08179
[2]
PubMed ID1631098
JournalProc Natl Acad Sci U S A
Year1992
Volume89
Pages6114-8
AuthorsAlmassy RJ, Janson CA, Kan CC, Hostomska Z
TitleStructures of apo and complexed Escherichia coli glycinamide ribonucleotide transformylase.
Related PDB1cdd,1cde
Related Swiss-protP08179
[3]
PubMed ID1522592
JournalJ Mol Biol
Year1992
Volume227
Pages283-92
AuthorsChen P, Schulze-Gahmen U, Stura EA, Inglese J, Johnson DL, Marolewski A, Benkovic SJ, Wilson IA
TitleCrystal structure of glycinamide ribonucleotide transformylase from Escherichia coli at 3.0 A resolution. A target enzyme for chemotherapy.
Related PDB1grc
Related Swiss-protP08179
[4]
PubMed ID7776369
JournalJ Mol Biol
Year1995
Volume249
Pages153-75
AuthorsKlein C, Chen P, Arevalo JH, Stura EA, Marolewski A, Warren MS, Benkovic SJ, Wilson IA
TitleTowards structure-based drug design: crystal structure of a multisubstrate adduct complex of glycinamide ribonucleotide transformylase at 1.96 A resolution.
Related PDB1gar
[5]
PubMed ID8688421
JournalBiochemistry
Year1996
Volume35
Pages8855-62
AuthorsWarren MS, Marolewski AE, Benkovic SJ
TitleA rapid screen of active site mutants in glycinamide ribonucleotide transformylase.
[6]
PubMed ID8876651
JournalJ Mol Biol
Year1996
Volume262
Pages746-55
AuthorsMullen CA, Jennings PA
TitleGlycinamide ribonucleotide transformylase undergoes pH-dependent dimerization.
[7]
PubMed ID9037007
JournalProc Natl Acad Sci U S A
Year1997
Volume94
Pages1069-73
AuthorsNixon AE, Warren MS, Benkovic SJ
TitleAssembly of an active enzyme by the linkage of two protein modules.
[8]
PubMed ID9354237
JournalBioorg Med Chem
Year1997
Volume5
Pages1817-30
AuthorsBoger DL, Haynes NE, Kitos PA, Warren MS, Ramcharan J, Marolewski AE, Benkovic SJ
Title10-Formyl-5,8,10-trideazafolic acid (10-formyl-TDAF): a potent inhibitor of glycinamide ribonucleotide transformylase.
[9]
PubMed ID9143358
JournalArch Biochem Biophys
Year1997
Volume341
Pages98-103
AuthorsCaperelli CA, Giroux EL
TitleThe human glycinamide ribonucleotide transformylase domain: purification, characterization, and kinetic mechanism.
[10]
PubMed ID9051735
JournalProtein Eng
Year1997
Volume10
Pages63-8
AuthorsWarren MS, Benkovic SJ
TitleCombinatorial manipulation of three key active site residues in glycinamide ribonucleotide transformylase.
[11]
PubMed ID9628739
JournalBiochemistry
Year1998
Volume37
Pages8776-82
AuthorsShim JH, Benkovic SJ
TitleEvaluation of the kinetic mechanism of Escherichia coli glycinamide ribonucleotide transformylase.
[12]
PubMed ID9698564
JournalJ Mol Biol
Year1998
Volume281
Pages485-99
AuthorsSu Y, Yamashita MM, Greasley SE, Mullen CA, Shim JH, Jennings PA, Benkovic SJ, Wilson IA
TitleA pH-dependent stabilization of an active site loop observed from low and high pH crystal structures of mutant monomeric glycinamide ribonucleotide transformylase at 1.8 to 1.9 A.
Related PDB2gar,3gar
Related Swiss-protP08179
[13]
PubMed ID9500916
JournalJ Mol Biol
Year1998
Volume276
Pages819-27
AuthorsMullen CA, Jennings PA
TitleA single mutation disrupts the pH-dependent dimerization of glycinamide ribonucleotide transformylase.
[14]
PubMed ID10606510
JournalBiochemistry
Year1999
Volume38
Pages16783-93
AuthorsGreasley SE, Yamashita MM, Cai H, Benkovic SJ, Boger DL, Wilson IA
TitleNew insights into inhibitor design from the crystal structure and NMR studies of Escherichia coli GAR transformylase in complex with beta-GAR and 10-formyl-5,8,10-trideazafolic acid.
Related PDB1c2t,1c3e
Related Swiss-protP08179
[15]
PubMed ID10433709
JournalBiochemistry
Year1999
Volume38
Pages10024-31
AuthorsShim JH, Benkovic SJ
TitleCatalytic mechanism of Escherichia coli glycinamide ribonucleotide transformylase probed by site-directed mutagenesis and pH-dependent studies.
[16]
PubMed ID10577357
JournalArch Biochem Biophys
Year1999
Volume370
Pages231-5
AuthorsAntle VD, Donat N, Hua M, Liao PL, Vince R, Carperelli CA
TitleSubstrate specificity of human glycinamide ribonucleotide transformylase.
[17]
PubMed ID10835105
JournalProtein Eng
Year2000
Volume13
Pages323-7
AuthorsNixon AE, Benkovic SJ
TitleImprovement in the efficiency of formyl transfer of a GAR transformylase hybrid enzyme.
[18]
PubMed ID11604542
JournalProtein Sci
Year2001
Volume10
Pages2363-78
AuthorsMorikis D, Elcock AH, Jennings PA, McCammon JA
TitleNative-state conformational dynamics of GART: a regulatory pH-dependent coil-helix transition examined by electrostatic calculations.
[19]
PubMed ID11604543
JournalProtein Sci
Year2001
Volume10
Pages2379-92
AuthorsMorikis D, Elcock AH, Jennings PA, McCammon JA
TitleProton transfer dynamics of GART: the pH-dependent catalytic mechanism examined by electrostatic calculations.
[20]
PubMed ID11695901
JournalBiochemistry
Year2001
Volume40
Pages13538-47
AuthorsGreasley SE, Marsilje TH, Cai H, Baker S, Benkovic SJ, Boger DL, Wilson IA
TitleUnexpected formation of an epoxide-derived multisubstrate adduct inhibitor on the active site of GAR transformylase.
Related PDB1jkx

comments
According to the literature [15], the catalytic reaction of this enzyme proceeds as follows:
(1) The transferred group, the formyl group of the CHO-THF substrate, is stabilized by the sidechains of His108 and Asn106. The imidazole ring of His108 is protonated by the interaction with Asp144.
(2) The acceptor group, the amine group of the GAR substrate, is in a free base form, and makes a nucleophilic attack on the formyl group, forming a tetrahedral intermediate.
(3) A proton transfer from the amine group of GAR to the leaving amine group is mediated by a catalytic water. This catalytic water may be assisted by Asp144.
(4) A breakdown of the tetrahedral intermediate leads to the release of products.

createdupdated
2002-05-012010-12-17


Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2010)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)

© Computational Biology Research Center, AIST, 2004 All Rights Reserved.