DB code: S00289

RLCP classification 3.943.131000.356 : Transfer
CATH domain 3.40.50.2020 : Rossmann fold Catalytic domain
E.C. 2.4.2.22
CSA 1a95
M-CSA 1a95
MACiE

CATH domain Related DB codes (homologues)
3.40.50.2020 : Rossmann fold S00288 S00287 D00131

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
P0A9M5 Xanthine phosphoribosyltransferase
EC 2.4.2.22
Xanthine-guanine phosphoribosyltransferase
XGPRT
NP_414773.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_488533.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
PF00156 (Pribosyltran)
[Graphical View]

KEGG enzyme name
xanthine 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

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P0A9M5 XGPT_ECOLI XMP + diphosphate = 5-phospho-alpha-D-ribose 1-diphosphate + xanthine. Homotetramer. Cell inner membrane, Peripheral membrane protein (Probable). Binds 1 magnesium ion per subunit.

KEGG Pathways
Map code Pathways E.C.
MAP00230 Purine metabolism

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00305 C00119 C00385 C00242 C00013 C00655 C00144
E.C.
Compound Magnesium 5-Phospho-alpha-D-ribose 1-diphosphate Xanthine Guanine Pyrophosphate (9-D-Ribosylxanthine)-5'-phosphate GMP
Type divalent metal (Ca2+, Mg2+) carbohydrate,phosphate group/phosphate ion amide group,aromatic ring (with nitrogen atoms) amide group,amine group,aromatic ring (with nitrogen atoms) phosphate group/phosphate ion amide group,nucleotide amide group,amine group,nucleotide
ChEBI 18420
17111
17712
48517
16235
29888
15652
17345
PubChem 888
7339
1188
764
1023
21961011
73323
6804
1a95A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1a95B Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_MG Analogue:PCP Unbound Bound:GUN Unbound Unbound Unbound
1a95C Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_MG Analogue:PCP Unbound Bound:GUN Unbound Unbound Unbound
1a95D Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1a96A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1a96B Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_MG Analogue:PCP Bound:XAN Unbound Unbound Unbound Unbound
1a96C Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_MG Analogue:PCP Bound:XAN Unbound Unbound Unbound Unbound
1a96D Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1a97A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1a97B Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Bound:5GP
1a97C Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Bound:5GP
1a97D Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1a98A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1a98B Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1nulA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_MG Unbound Unbound Unbound Unbound Unbound Unbound
1nulB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_MG Unbound Unbound Unbound Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
literature [3]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1a95A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 88;ASP 89;ASP 92 ASP 89(magnesium binding)
1a95B Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 88;ASP 89;ASP 92 ASP 89(magnesium binding)
1a95C Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 88;ASP 89;ASP 92 ASP 89(magnesium binding)
1a95D Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 88;ASP 89;ASP 92 ASP 89(magnesium binding)
1a96A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 88;ASP 89;ASP 92 ASP 89(magnesium binding)
1a96B Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 88;ASP 89;ASP 92 ASP 89(magnesium binding)
1a96C Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 88;ASP 89;ASP 92 ASP 89(magnesium binding)
1a96D Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 88;ASP 89;ASP 92 ASP 89(magnesium binding)
1a97A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 88;ASP 89;ASP 92 ASP 89(magnesium binding)
1a97B Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 88;ASP 89;ASP 92 ASP 89(magnesium binding)
1a97C Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 88;ASP 89;ASP 92 ASP 89(magnesium binding)
1a97D Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 88;ASP 89;ASP 92 ASP 89(magnesium binding)
1a98A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 88;ASP 89;ASP 92 ASP 89(magnesium binding)
1a98B Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 88;ASP 89;ASP 92 ASP 89(magnesium binding)
1nulA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 88;ASP 89;ASP 92 ASP 89(magnesium binding)
1nulB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 88;ASP 89;ASP 92 ASP 89(magnesium binding)

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[3]
p.885

References
[1]
Resource
Comments
Medline ID
PubMed ID 8812991
Journal J Struct Biol
Year 1996
Volume 116
Pages 330-4
Authors Vos S, de Jersey J, Martin JL
Title Crystallization and preliminary X-ray crystallographic studies of Escherichia coli xanthine phosphoribosyltransferase.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 9100006
Journal Biochemistry
Year 1997
Volume 36
Pages 4125-34
Authors Vos S, de Jersey J, Martin JL
Title Crystal structure of Escherichia coli xanthine phosphoribosyltransferase.
Related PDB 1nul
Related UniProtKB P0A9M5
[3]
Resource
Comments
Medline ID
PubMed ID 9743633
Journal J Mol Biol
Year 1998
Volume 282
Pages 875-89
Authors Vos S, Parry RJ, Burns MR, de Jersey J, Martin JL
Title Structures of free and complexed forms of Escherichia coli xanthine-guanine phosphoribosyltransferase.
Related PDB 1a95 1a96 1a97 1a98
Related UniProtKB P0A9M5

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.

Created Updated
2002-05-02 2009-02-26