EzCatDB: S00289

DB codeS00289
RLCP classification3.943.131000.356
CATH domainDomain 13.40.50.2020Catalytic domain
E.C.2.4.2.22
CSA1a95

CATH domainRelated DB codes (homologues)
3.40.50.2020S00288,S00287,D00131

Enzyme Name
Swiss-protKEGG

P0A9M5
Protein nameXanthine phosphoribosyltransferasexanthine phosphoribosyltransferase
Xan phosphoribosyltransferase
xanthosine 5'-phosphate pyrophosphorylase
xanthylate pyrophosphorylase
xanthylic pyrophosphorylase
XMP pyrophosphorylase
5-phospho-alpha-D-ribose-1-diphosphate:xanthinephospho-D-ribosyltransferase
9-(5-phospho-beta-D-ribosyl)xanthine:diphosphate5-phospho-alpha-D-ribosyltransferase
SynonymsEC 2.4.2.22
Xanthine-guanine phosphoribosyltransferase
XGPRT

KEGG pathways
MAP codePathways
MAP00230Purine metabolism

Swiss-prot:Accession NumberP0A9M5
Entry nameXGPT_ECOLI
ActivityXMP + diphosphate = 5-phospho-alpha-D-ribose 1-diphosphate + xanthine.
SubunitHomotetramer.
Subcellular locationCell inner membrane, Peripheral membrane protein (Probable).
CofactorBinds 1 magnesium ion per subunit.


CofactorsSubstratesProducts
KEGG-idC00305C00119C00385C00242C00013C00655C00144
CompoundMagnesium5-Phospho-alpha-D-ribose 1-diphosphateXanthineGuaninePyrophosphate(9-D-Ribosylxanthine)-5'-phosphateGMP
Typedivalent metal (Ca2+, Mg2+)carbohydrate,phosphate group/phosphate ionamide group,aromatic ring (with nitrogen atoms)amide group,amine group,aromatic ring (with nitrogen atoms)phosphate group/phosphate ionamide group,nucleotideamide group,amine group,nucleotide
1a95AUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1a95BBound:_MGAnalogue:PCPUnboundBound:GUNUnboundUnboundUnbound
1a95CBound:_MGAnalogue:PCPUnboundBound:GUNUnboundUnboundUnbound
1a95DUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1a96AUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1a96BBound:_MGAnalogue:PCPBound:XANUnboundUnboundUnboundUnbound
1a96CBound:_MGAnalogue:PCPBound:XANUnboundUnboundUnboundUnbound
1a96DUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1a97AUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1a97BUnboundUnboundUnboundUnboundUnboundUnboundBound:5GP
1a97CUnboundUnboundUnboundUnboundUnboundUnboundBound:5GP
1a97DUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1a98AUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1a98BUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1nulABound:_MGUnboundUnboundUnboundUnboundUnboundUnbound
1nulBBound:_MGUnboundUnboundUnboundUnboundUnboundUnbound

Active-site residues
resource
literature [3]
pdbCatalytic residuesCofactor-binding residues
1a95AASP 88;ASP 89;ASP 92
ASP 89(magnesium binding)
1a95BASP 88;ASP 89;ASP 92
ASP 89(magnesium binding)
1a95CASP 88;ASP 89;ASP 92
ASP 89(magnesium binding)
1a95DASP 88;ASP 89;ASP 92
ASP 89(magnesium binding)
1a96AASP 88;ASP 89;ASP 92
ASP 89(magnesium binding)
1a96BASP 88;ASP 89;ASP 92
ASP 89(magnesium binding)
1a96CASP 88;ASP 89;ASP 92
ASP 89(magnesium binding)
1a96DASP 88;ASP 89;ASP 92
ASP 89(magnesium binding)
1a97AASP 88;ASP 89;ASP 92
ASP 89(magnesium binding)
1a97BASP 88;ASP 89;ASP 92
ASP 89(magnesium binding)
1a97CASP 88;ASP 89;ASP 92
ASP 89(magnesium binding)
1a97DASP 88;ASP 89;ASP 92
ASP 89(magnesium binding)
1a98AASP 88;ASP 89;ASP 92
ASP 89(magnesium binding)
1a98BASP 88;ASP 89;ASP 92
ASP 89(magnesium binding)
1nulAASP 88;ASP 89;ASP 92
ASP 89(magnesium binding)
1nulBASP 88;ASP 89;ASP 92
ASP 89(magnesium binding)

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[3]p.885

references
[1]
PubMed ID8812991
JournalJ Struct Biol
Year1996
Volume116
Pages330-4
AuthorsVos S, de Jersey J, Martin JL
TitleCrystallization and preliminary X-ray crystallographic studies of Escherichia coli xanthine phosphoribosyltransferase.
[2]
PubMed ID9100006
JournalBiochemistry
Year1997
Volume36
Pages4125-34
AuthorsVos S, de Jersey J, Martin JL
TitleCrystal structure of Escherichia coli xanthine phosphoribosyltransferase.
Related PDB1nul
Related Swiss-protP0A9M5
[3]
PubMed ID9743633
JournalJ Mol Biol
Year1998
Volume282
Pages875-89
AuthorsVos S, Parry RJ, Burns MR, de Jersey J, Martin JL
TitleStructures of free and complexed forms of Escherichia coli xanthine-guanine phosphoribosyltransferase.
Related PDB1a95,1a96,1a97,1a98
Related Swiss-protP0A9M5

comments
According to the literature [3], the catalytic reaction of this enzyme seems to proceed via an SN1 mechanism, forming an oxocarbonium ion in the transition state. The oxocarbonium ion of ribosyl group may adopt C3 pucker with a planar geometry at C1 position, which is promoted by magnesium ion that interacts with oxygen atoms of the leaving pyrophosphate group and the ribose hydroxyl groups. This positively charged transition-state intermediate can be stabilized by the conserved aspartic acid residues, Asp88 and Asp89, through electrostatic interactions. In contrast, without substrate or product molecules in the active site, magnesium ion is bound to Asp89.
Meanwhile, the sidechain of Asp92 can act as a general base, which abstracts proton from N7 atom of the substrate purine base (see [3]). The deprotonated purine base might react with the C1 atom of the transferred ribosyl group, to produce the purine mononucleotide.

createdupdated
2002-05-022009-02-26
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)

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