EzCatDB: T00114

DB codeT00114
RLCP classification1.13.30000.42
3.123.90030.312
CATH domainDomain 13.40.50.880Catalytic domain
Domain 23.40.50.620Catalytic domain
Domain 33.30.300.10
E.C.6.3.5.2
CSA1gpm
MACiEM0234

CATH domainRelated DB codes (homologues)
3.40.50.620S00314,S00549,S00316,S00317,S00318,S00315,T00085,T00249,D00300,M00177,M00178,T00106
3.40.50.880D00526,T00021,M00215

Enzyme Name
Swiss-protKEGG

P04079
Protein nameGMP synthase {glutamine-hydrolyzing}GMP synthase (glutamine-hydrolysing)
GMP synthetase (glutamine-hydrolysing)
guanylate synthetase (glutamine-hydrolyzing)
guanosine monophosphate synthetase (glutamine-hydrolyzing)
xanthosine 5'-phosphate amidotransferase
guanosine 5'-monophosphate synthetase
SynonymsEC 6.3.5.2
Glutamine amidotransferase
GMP synthetase
GMPS

KEGG pathways
MAP codePathways
MAP00230Purine metabolism
MAP00251Glutamate metabolism
MAP00983Drug metabolism - other enzymes

Swiss-prot:Accession NumberP04079
Entry nameGUAA_ECOLI
ActivityATP + xanthosine 5''-phosphate + L-glutamine + H(2)O = AMP + diphosphate + GMP + L-glutamate.
SubunitHomodimer.
Subcellular location
Cofactor


CofactorsSubstratesProducts
KEGG-idC00305C00002C00655C00064C00001C00020C00013C00144C00025
CompoundMagnesiumATPXanthosine 5'-phosphateL-GlutamineH2OAMPPyrophosphateGMPL-Glutamate
Typedivalent metal (Ca2+, Mg2+)amine group,nucleotideamide group,nucleotideamino acids,amide groupH2Oamine group,nucleotidephosphate group/phosphate ionamide group,amine group,nucleotideamino acids,carboxyl group
1gpmA01UnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnbound
1gpmB01UnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnbound
1gpmC01UnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnbound
1gpmD01UnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnbound
1gpmA02UnboundUnboundUnboundUnbound
Bound:AMPBound:POPUnboundUnbound
1gpmB02Bound:_MGUnboundUnboundUnbound
Bound:AMPBound:POPUnboundUnbound
1gpmC02Bound:_MGUnboundUnboundUnbound
Bound:AMPBound:POPUnboundUnbound
1gpmD02Bound:_MGUnboundUnboundUnbound
Bound:AMPBound:POPUnboundUnbound
1gpmA03UnboundUnboundUnboundUnbound
UnboundAnalogue:PO4UnboundUnbound
1gpmB03UnboundUnboundUnboundUnbound
UnboundAnalogue:PO4UnboundUnbound
1gpmC03UnboundUnboundUnboundUnbound
UnboundAnalogue:PO4UnboundUnbound
1gpmD03UnboundUnboundUnboundUnbound
UnboundAnalogue:PO4UnboundUnbound

Active-site residues
resource
Swiss-prot;P04079, literature [6]
pdbCatalytic residuesCofactor-binding residuesMain-chain involved in catalysis
1gpmA01CYS 86;HIS 181;GLU 183

GLY 59;TYR 87;GLY 88
1gpmB01CYS 86;HIS 181;GLU 183

GLY 59;TYR 87;GLY 88
1gpmC01CYS 86;HIS 181;GLU 183

GLY 59;TYR 87;GLY 88
1gpmD01CYS 86;HIS 181;GLU 183

GLY 59;TYR 87;GLY 88
1gpmA02SER 235;SER 240;LYS 381
ASP 239(Magnesium binding)
GLY 236;GLY 237
1gpmB02SER 235;SER 240;LYS 381
ASP 239(Magnesium binding)
GLY 236;GLY 237
1gpmC02SER 235;SER 240;LYS 381
ASP 239(Magnesium binding)
GLY 236;GLY 237
1gpmD02SER 235;SER 240;LYS 381
ASP 239(Magnesium binding)
GLY 236;GLY 237
1gpmA03


1gpmB03


1gpmC03


1gpmD03



References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[1]Fig.11, p.26462
[6]Fig.1, p.752
[8]Scheme 3

references
[1]
PubMed ID6378670
JournalFed Proc
Year1984
Volume43
Pages2640-7
AuthorsVillafranca JJ
TitleUse of 31P and 13C NMR to study enzyme mechanisms.
[2]
CommentsGATASE DOMAIN.
Medline ID85131126
PubMed ID2982857
JournalJ Biol Chem
Year1985
Volume260
Pages3350-4
AuthorsZalkin H, Argos P, Narayana SV, Tiedeman AA, Smith JM
TitleIdentification of a trpG-related glutamine amide transfer domain in Escherichia coli GMP synthetase.
Related Swiss-protP04079
[3]
PubMed ID3911001
JournalMethods Enzymol
Year1985
Volume113
Pages273-8
AuthorsZalkin H
TitleGMP synthetase.
[4]
PubMed ID8208731
JournalProteins
Year1994
Volume18
Pages394-403
AuthorsTesmer JJ, Stemmler TL, Penner-Hahn JE, Davisson VJ, Smith JL
TitlePreliminary X-ray analysis of Escherichia coli GMP synthetase: determination of anomalous scattering factors for a cysteinyl mercury derivative.
[5]
PubMed ID8895556
JournalEMBO J
Year1996
Volume15
Pages5125-34
AuthorsRizzi M, Nessi C, Mattevi A, Coda A, Bolognesi M, Galizzi A
TitleCrystal structure of NH3-dependent NAD+ synthetase from Bacillus subtilis.
[6]
CommentsX-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS).
Medline ID96133732
PubMed ID8548458
JournalNat Struct Biol
Year1996
Volume3
Pages74-86
AuthorsTesmer JJ, Klem TJ, Deras ML, Davisson VJ, Smith JL
TitleThe crystal structure of GMP synthetase reveals a novel catalytic triad and is a structural paradigm for two enzyme families.
Related PDB1gpm
Related Swiss-protP04079
[7]
PubMed ID11395405
JournalAnnu Rev Biochem
Year2001
Volume70
Pages149-80
AuthorsHuang X, Holden HM, Raushel FM
TitleChanneling of substrates and intermediates in enzyme-catalyzed reactions.
[8]
PubMed ID11170408
JournalBiochemistry
Year2001
Volume40
Pages876-87
AuthorsChittur SV, Klem TJ, Shafer CM, Davisson VJ
TitleMechanism for acivicin inactivation of triad glutamine amidotransferases.

comments
According to the literature [6], [7], separate reactions occur at the N-terminal glutaminase domain (CATH 3.40.50.880) and at the ATP pyrophosphatase domain (CATH 3.40.50.620).
At the N-terminal glutaminase domain, which contains a catalytic triad (Cys86/His181/Glu183) and an oxyanion hole (composed of mainchain amide of Gly59/Tyr88/Gly88), hydrolysis of the sidechain amide of glutamine occurs by the trypsin-like reaction mechanism (see [6] & [8]).
(1) Cys86 acts as a nucleophile to make an attack on the carbonyl carbon. His181 and Glu183 assist this reaction.
(2) The transient negative charge on the intermediate will be stabilized by the oxyanion hole.
(3) A water molecule, activated by His181, may hydrolyze the intermediate.
At the ATP pyrophosphatase domain, two successive transfer reactions, transfer of AMP to carbonyl oxygen (O2 atom) of the XMP base, and transfer of the purine nucleotide to amine of ammonia molecule, released by the N-terminal domain.
According to the active-site structure and the data of the homologous enzyme (S00315 in EzCatDB), the transfer reaction of AMP to the carbonyl oxygen of XMP proceeds, probably as follows:
(A1) Mg2+ ion, Ser235, Gly236, Gly237 and Ser240 from P-loop and Lys381 stabilizes the leaving pyrophosphate, by neutralizing the negative charges, and also activate the transferred group, alpha-phosphate of ATP, by enhancing the electrophilicity of the phosphate group through polarization.
(A2) The acceptor group, the carbonyl oxygen (O2) atom of the XMP base, makes a nucleophilic attack on the transferred group, the alpha-phosphate of ATP.
(A3) The Mg2+ ion stabilize the pentacovalent transition-state.
(A4) O2-Adenyl-XMP intermediate is formed, releasing the pyrophosphate.
The detailed mechanism of the transfer of the nucleotide to amine of the ammonia molecule has not been elucidated. However, it will probably proceeds as follows:
(B1) Some group must act as a general base, to deprotonate the ammonium ion. However, it is not clear which group will activate the ammonium ion. (Probably, the remaining pyrophosphate or Asp340, considering the structure)
(B2) The activated ammonium makes a nucleophilic attack on the C2 atom of the O2-adenyl-XMP intermediate, forming a tetrahedral transition-state adduct.
(B3) Some group must stabilize the tetrahedral transition-state. However, it is not clear which group is involved in the stabilization. Mg2+ ion will stabilize the leaving phosphate of AMP.
(B4) Finally, GMP and AMP are formed.
More biochemical data will be required, to elucidate the mechanism.

createdupdated
2004-09-272009-02-26
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)

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