EzCatDB: S00287

DB codeS00287
RLCP classification3.943.120000.356
CATH domainDomain 13.40.50.2020Catalytic domain
E.C.2.4.2.9
CSA1bd3

CATH domainRelated DB codes (homologues)
3.40.50.2020S00288,S00289,D00131

Enzyme Name
Swiss-protKEGG

Q26998P70881
Protein nameUracil phosphoribosyltransferaseUracil phosphoribosyltransferaseuracil phosphoribosyltransferase
UMP pyrophosphorylase
UPRTase
UMP:pyrophosphate phosphoribosyltransferase
uridine 5'-phosphate pyrophosphorylase
uridine monophosphate pyrophosphorylase
uridylate pyrophosphorylase
uridylic pyrophosphorylase
SynonymsEC 2.4.2.9
UMP pyrophosphorylase
UPRTase
UPRT
EC 2.4.2.9
UMP pyrophosphorylase
UPRTase

KEGG pathways
MAP codePathways
MAP00240Pyrimidine metabolism

Swiss-prot:Accession NumberQ26998P70881
Entry nameUPP_TOXGOUPP_BACCL
ActivityUMP + diphosphate = uracil + 5-phospho-alpha- D-ribose 1-diphosphate.UMP + diphosphate = uracil + 5-phospho-alpha- D-ribose 1-diphosphate.
SubunitMonomer.Homodimer.
Subcellular location

Cofactor
Magnesium (By similarity).


CofactorsSubstratesProducts
KEGG-idC00305C00106C00119C00105C00013
CompoundmagnesiumUracil5-Phospho-alpha-D-ribose 1-diphosphateUMPPyrophosphate
Typedivalent metal (Ca2+, Mg2+)amide group,aromatic ring (with nitrogen atoms)carbohydrate,phosphate group/phosphate ionamide group,nucleotidephosphate group/phosphate ion
1bd3AUnboundUnboundUnboundUnboundUnbound
1bd3BUnboundUnboundUnboundUnboundUnbound
1bd3CUnboundUnboundUnboundUnboundUnbound
1bd3DUnboundUnboundUnboundUnboundUnbound
1bd4AUnboundBound:URAUnboundUnboundUnbound
1bd4BUnboundBound:URAUnboundUnboundUnbound
1bd4CUnboundBound:URAUnboundUnboundUnbound
1bd4DUnboundBound:URAUnboundUnboundUnbound
1upfAUnboundAnalogue:URFUnboundUnboundAnalogue:SO4
1upfBUnboundAnalogue:URFUnboundUnboundAnalogue:SO4
1upfCUnboundAnalogue:URFUnboundUnboundAnalogue:SO4
1upfDUnboundAnalogue:URFUnboundUnboundAnalogue:SO4
1upuAUnboundUnboundUnboundBound:U5PUnbound
1upuBUnboundUnboundUnboundBound:U5PUnbound
1upuCUnboundUnboundUnboundBound:U5PUnbound
1upuDUnboundUnboundUnboundBound:U5PUnbound
1jlrAUnboundUnboundUnboundUnboundAnalogue:PO4
1jlrBUnboundUnboundUnboundUnboundAnalogue:PO4
1jlrCUnboundUnboundUnboundUnboundAnalogue:PO4
1jlrDUnboundUnboundUnboundUnboundAnalogue:PO4
1jlsAUnboundBound:URAUnboundUnboundAnalogue:PO4
1jlsBBound:_MGBound:URABound:PRPUnboundUnbound
1jlsCUnboundBound:URAUnboundUnboundUnbound
1jlsDUnboundBound:URAUnboundUnboundAnalogue:PO4
1i5eAUnboundUnboundUnboundBound:U5PUnbound
1i5eBUnboundUnboundUnboundBound:U5PUnbound

Active-site residues
pdbCatalytic residues
1bd3AASP 164;ASP 235;ASP 238
1bd3BASP 164;ASP 235;ASP 238
1bd3CASP 164;ASP 235;ASP 238
1bd3DASP 164;ASP 235;ASP 238
1bd4AASP 164;ASP 235;ASP 238
1bd4BASP 164;ASP 235;ASP 238
1bd4CASP 164;ASP 235;ASP 238
1bd4DASP 164;ASP 235;ASP 238
1upfAASP 164;ASP 235;ASP 238
1upfBASP 164;ASP 235;ASP 238
1upfCASP 164;ASP 235;ASP 238
1upfDASP 164;ASP 235;ASP 238
1upuAASP 164;ASP 235;ASP 238
1upuBASP 164;ASP 235;ASP 238
1upuCASP 164;ASP 235;ASP 238
1upuDASP 164;ASP 235;ASP 238
1jlrAASP 164;ASP 235;ASP 238
1jlrBASP 164;ASP 235;ASP 238
1jlrCASP 164;ASP 235;ASP 238
1jlrDASP 164;ASP 235;ASP 238
1jlsAASP 164;ASP 235;ASP 238
1jlsBASP 164;ASP 235;ASP 238
1jlsCASP 164;ASP 235;ASP 238
1jlsDASP 164;ASP 235;ASP 238
1i5eAASP 131;ASP 200;ASP 203
1i5eBASP 131;ASP 200;ASP 203

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[3]p.3228-3229
[5]p.81-83
[6]p.943-944, Fig.81

references
[1]
PubMed ID8080452
JournalBiochem Pharmacol
Year1994
Volume48
Pages781-92
AuthorsIltzsch MH, Tankersley KO
TitleStructure-activity relationship of ligands of uracil phosphoribosyltransferase from Toxoplasma gondii.
[2]
PubMed ID8765224
JournalBiochim Biophys Acta
Year1996
Volume1296
Pages16-22
AuthorsLinde L, Jensen KF
TitleUracil phosphoribosyltransferase from the extreme thermoacidophilic archaebacterium Sulfolobus shibatae is an allosteric enzyme, activated by GTP and inhibited by CTP.
[3]
PubMed ID9628859
JournalEMBO J
Year1998
Volume17
Pages3219-32
AuthorsSchumacher MA, Carter D, Scott DM, Roos DS, Ullman B, Brennan RG
TitleCrystal structures of Toxoplasma gondii uracil phosphoribosyltransferase reveal the atomic basis of pyrimidine discrimination and prodrug binding.
Related PDB1bd3,1bd4,1upf,1upu
Related Swiss-protQ26998
[4]
PubMed ID10079076
JournalBiochemistry
Year1999
Volume38
Pages3327-34
AuthorsLundegaard C, Jensen KF
TitleKinetic mechanism of uracil phosphoribosyltransferase from Escherichia coli and catalytic importance of the conserved proline in the PRPP binding site.
[5]
PubMed ID11773618
JournalProc Natl Acad Sci U S A
Year2002
Volume99
Pages78-83
AuthorsSchumacher MA, Bashor CJ, Song MH, Otsu K, Zhu S, Parry RJ, Ullman B, Brennan RG
TitleThe structural mechanism of GTP stabilized oligomerization and catalytic activation of the Toxoplasma gondii uracil phosphoribosyltransferase.
Related PDB1jlr,1jls
[6]
PubMed ID12037295
JournalActa Crystallogr D Biol Crystallogr
Year2002
Volume58
Pages936-45
AuthorsKadziola A, Neuhard J, Larsen S
TitleStructure of product-bound Bacillus caldolyticus uracil phosphoribosyltransferase confirms ordered sequential substrate binding.
Related PDB1i5e
[7]
PubMed ID12482852
JournalJ Biol Chem
Year2003
Volume278
Pages6921-7
AuthorsGrabner GK, Switzer RL
TitleKinetic studies of the uracil phosphoribosyltransferase reaction catalyzed by the Bacillus subtilis pyrimidine attenuation regulatory protein PyrR.

comments
According to the literature [6], one of the substrates, uracil can adopt its tautomeric enol form, with a hydroxyl group at O2 protonated from N1 atom. This enol form of uracil can donate the proton to the carboxylate of Asp235 (Asp200 at PDB 1i5e), acting as a general base, and the alpha-phosphate group of another substrate, PRPP. The movement of the proton towards OP1 of the alpha-phosphate of PRPP activates uracil itself as a nucleophile and the pyrophosphate of PRPP as a leaving group.
The paper [5] also suggested that Asp235 might act as the general base, or a proton shuttle, whilst the paper itself also suggested substrate-assisted abstraction of N1 proton of uracil by alpha-phosphate of PRPP. Moreover, Asp238 increased the pKa of the sidechain of Asp235, which can abstract a proton from the scissile pyrophosphate.
Moreover, the paper [6] suggested that Asp164 (Asp131 at 1i5e) might stabilize the positively charged oxocarbenium-like transition state.
Although the reaction seems to be dependent on magnesium, its role has not been elucidated. As it seems to be bound to beta-phosphate group of PRPP (PDB 1jls), it may contribute to the leaving group.
The reaction between the uracil N1 nucleophile and the PRPP C1' atom might proceed through an SN1 or SN2-like mechanism, or mixture of these mechanisms, to produce UMP and pyrophosphate, according to the paper [5].

createdupdated
2002-05-022009-03-30


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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