EzCatDB: S00221

DB codeS00221
CATH domainDomain 13.20.20.70Catalytic domain
E.C.4.1.1.23
CSA1dbt,1eix
MACiEM0050

CATH domainRelated DB codes (homologues)
3.20.20.70S00215,S00217,S00218,S00219,S00532,S00198,S00220,S00745,S00537,S00538,S00539,S00826,S00841,S00235,S00239,S00240,S00243,S00244,S00199,S00200,S00201,S00222,S00847,S00224,S00225,S00226,D00014,D00029,M00141,T00015,T00239,D00664,D00665,D00804,D00863,T00089

Enzyme Name
Swiss-protKEGG

O26232P03962P25971P08244
Protein nameOrotidine 5''-phosphate decarboxylaseOrotidine 5''-phosphate decarboxylaseOrotidine 5''-phosphate decarboxylaseOrotidine 5''-phosphate decarboxylaseorotidine-5'-phosphate decarboxylase
orotidine-5'-monophosphate decarboxylase
orotodylate decarboxylase
orotidine phosphate decarboxylase
OMP decarboxylase
orotate monophosphate decarboxylase
orotidine monophosphate decarboxylase
orotidine phosphate decarboxylase
OMP-DC
orotate decarboxylase
orotidine 5'-phosphate decarboxylase
orotidylic decarboxylase
orotidylic acid decarboxylase
orotodylate decarboxylase
ODCase
orotic decarboxylase
orotidine-5'-phosphate carboxy-lyase
SynonymsEC 4.1.1.23
OMP decarboxylase
OMPDCase
OMPdecase
EC 4.1.1.23
OMP decarboxylase
OMPdecase
OMPDCase
Uridine 5''-monophosphate synthase
UMP synthase
EC 4.1.1.23
OMP decarboxylase
OMPDCase
OMPdecase
EC 4.1.1.23
OMP decarboxylase
OMPDCase
OMPdecase

KEGG pathways
MAP codePathways
MAP00240Pyrimidine metabolism

Swiss-prot:Accession NumberO26232P03962P25971P08244
Entry namePYRF_METTHPYRF_YEASTPYRF_BACSUPYRF_ECOLI
ActivityOrotidine 5''-phosphate = UMP + CO(2).Orotidine 5''-phosphate = UMP + CO(2).Orotidine 5''-phosphate = UMP + CO(2).Orotidine 5''-phosphate = UMP + CO(2).
SubunitHomodimer.
Homodimer.Homodimer.
Subcellular location



Cofactor





SubstratesProductsintermediates
KEGG-idC01103C00105C00011
CompoundOrotidine 5'-phosphateUMPCO2literature
Typeamide group,carbohydrate,nucleotideamide group,nucleotideothersreffernce[18]
1dbtAUnboundBound:U5PUnboundUnbound
1dbtBUnboundBound:U5PUnboundUnbound
1dbtCUnboundBound:U5PUnboundUnbound
1dqwAUnboundUnboundUnboundUnbound
1dqwBUnboundUnboundUnboundUnbound
1dqwCUnboundUnboundUnboundUnbound
1dqwDUnboundUnboundUnboundUnbound
1dqxAUnboundUnboundUnboundTransition-state-analogue:BMP
1dqxBUnboundUnboundUnboundTransition-state-analogue:BMP
1dqxCUnboundUnboundUnboundTransition-state-analogue:BMP
1dqxDUnboundUnboundUnboundTransition-state-analogue:BMP
1dv7AUnboundUnboundUnboundUnbound
1dvjAUnboundAnalogue:UP6UnboundUnbound
1dvjBUnboundAnalogue:UP6UnboundUnbound
1dvjCUnboundAnalogue:UP6UnboundUnbound
1dvjDUnboundAnalogue:UP6UnboundUnbound
1eixAAnalogue:BMQUnboundUnboundUnbound
1eixBAnalogue:BMQUnboundUnboundUnbound
1eixCAnalogue:BMQUnboundUnboundUnbound
1eixDAnalogue:BMQUnboundUnboundUnbound
1jjkAUnboundUnboundUnboundTransition-state-analogue:BMP
1jjkBUnboundUnboundUnboundTransition-state-analogue:BMP
1jjkCUnboundUnboundUnboundTransition-state-analogue:BMP
1jjkDUnboundUnboundUnboundTransition-state-analogue:BMP
1jjkEUnboundUnboundUnboundTransition-state-analogue:BMP
1jjkFUnboundUnboundUnboundTransition-state-analogue:BMP
1jjkGUnboundUnboundUnboundTransition-state-analogue:BMP
1jjkHUnboundUnboundUnboundTransition-state-analogue:BMP
1jjkIUnboundUnboundUnboundTransition-state-analogue:BMP
1jjkJUnboundUnboundUnboundTransition-state-analogue:BMP
1jjkKUnboundUnboundUnboundTransition-state-analogue:BMP
1jjkLUnboundUnboundUnboundTransition-state-analogue:BMP
1jjkMUnboundUnboundUnboundTransition-state-analogue:BMP
1jjkNUnboundUnboundUnboundTransition-state-analogue:BMP
1jjkOUnboundUnboundUnboundTransition-state-analogue:BMP
1jjkPUnboundUnboundUnboundTransition-state-analogue:BMP
1l2uAUnboundUnboundUnboundUnbound
1l2uBUnboundUnboundUnboundUnbound

Active-site residues
resource
Swiss-prot;O26232, P03962, P25971
pdbCatalytic residues
1dbtALYS 62
1dbtBLYS 62
1dbtCLYS 62
1dqwALYS 93
1dqwBLYS 93
1dqwCLYS 93
1dqwDLYS 93
1dqxALYS 93
1dqxBLYS 93
1dqxCLYS 93
1dqxDLYS 93
1dv7ALYS 72
1dvjALYS 72
1dvjBLYS 72
1dvjCLYS 72
1dvjDLYS 72
1eixALYS 73
1eixBLYS 73
1eixCLYS 73
1eixDLYS 73
1jjkALYS 73
1jjkBLYS 73
1jjkCLYS 73
1jjkDLYS 73
1jjkELYS 73
1jjkFLYS 73
1jjkGLYS 73
1jjkHLYS 73
1jjkILYS 73
1jjkJLYS 73
1jjkKLYS 73
1jjkLLYS 73
1jjkMLYS 73
1jjkNLYS 73
1jjkOLYS 73
1jjkPLYS 73
1l2uALYS 73
1l2uBLYS 73

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[6]p.12167-12168
[7]p.336-341
[9]

[11]Fig.6, Fig.7, p.4222-42242
[12]p.8116-8117
[14]Fig.3, Fig.4, Fig.5, p.4572-4574
[15]p.14731-14733
[16]Fig.2, p.714-716
[17]Scheme 1, Fig.7, p.2009-20102
[18]Fig.7, p.2014-20163
[19]Scheme II, p.2020-20223
[20]

[22]Fig.1, Fig.2, p.104-105
[23]Scheme 3, Scheme 4, p.114-118
[24]Fig.12, p.12846-12848
[26]Fig.8, p.863-874
[32]Fig. 1p.268

references
[1]
PubMed ID6894094
JournalBiochemistry
Year1980
Volume19
Pages6068-74
AuthorsTraut TW, Payne RC
TitleDependence of the catalytic activities on the aggregation and conformation states of uridine 5'-phosphate synthase.
[2]
PubMed ID6894093
JournalBiochemistry
Year1980
Volume19
Pages6062-8
AuthorsTraut TW, Payne RC, Jones ME
TitleDependence of the aggregation and conformation states of uridine 5'-phosphate synthase on pyrimidine nucleotides. Evidence for a regulatory site.
[3]
PubMed ID2334689
JournalBiochemistry
Year1990
Volume29
Pages3198-202
AuthorsAcheson SA, Bell JB, Jones ME, Wolfenden R
TitleOrotidine-5'-monophosphate decarboxylase catalysis: kinetic isotope effects and the state of hybridization of a bound transition-state analogue.
[4]
PubMed ID2008434
JournalProteins
Year1991
Volume9
Pages143-51
AuthorsBell JB, Jones ME, Carter CW Jr
TitleCrystallization of yeast orotidine 5'-monophosphate decarboxylase complexed with 1-(5'-phospho-beta-D-ribofuranosyl) barbituric acid.
[5]
PubMed ID1457411
JournalBiochemistry
Year1992
Volume31
Pages12155-61
AuthorsShostak K, Jones ME
TitleOrotidylate decarboxylase: insights into the catalytic mechanism from substrate specificity studies.
[6]
PubMed ID1457412
JournalBiochemistry
Year1992
Volume31
Pages12162-8
AuthorsSmiley JA, Jones ME
TitleA unique catalytic and inhibitor-binding role for Lys93 of yeast orotidylate decarboxylase.
[7]
PubMed ID1499340
JournalCurr Top Cell Regul
Year1992
Volume33
Pages331-42
AuthorsJones ME
TitleOrotidylate decarboxylase of yeast and man.
[8]
PubMed ID8631878
JournalJ Biol Chem
Year1996
Volume271
Pages10704-8
AuthorsYablonski MJ, Pasek DA, Han BD, Jones ME, Traut TW
TitleIntrinsic activity and stability of bifunctional human UMP synthase and its two separate catalytic domains, orotate phosphoribosyltransferase and orotidine-5'-phosphate decarboxylase.
[9]
PubMed ID9139656
JournalScience
Year1997
Volume276
Pages942-5
AuthorsLee JK, Houk KN
TitleA proficient enzyme revisited: the predicted mechanism for orotidine monophosphate decarboxylase.
[10]
PubMed ID10334928
JournalBiochem Biophys Res Commun
Year1999
Volume259
Pages133-5
AuthorsCui W, DeWitt JG, Miller SM, Wu W
TitleNo metal cofactor in orotidine 5'-monophosphate decarboxylase.
[11]
CommentsX-ray crystallography
PubMed ID10757968
JournalBiochemistry
Year2000
Volume39
Pages4217-24
AuthorsHarris P, Navarro Poulsen JC, Jensen KF, Larsen S
TitleStructural basis for the catalytic mechanism of a proficient enzyme: orotidine 5'-monophosphate decarboxylase.
Related PDB1eix
[12]
PubMed ID10889016
JournalBiochemistry
Year2000
Volume39
Pages8113-8
AuthorsMiller BG, Snider MJ, Short SA, Wolfenden R
TitleContribution of enzyme-phosphoribosyl contacts to catalysis by orotidine 5'-phosphate decarboxylase.
[13]
PubMed ID10995247
JournalBiochemistry
Year2000
Volume39
Pages11788-800
AuthorsPorter DJ, Short SA
TitleYeast orotidine-5'-phosphate decarboxylase: steady-state and pre-steady-state analysis of the kinetic mechanism of substrate decarboxylation.
[14]
PubMed ID10769111
JournalBiochemistry
Year2000
Volume39
Pages4569-74
AuthorsRishavy MA, Cleland WW
TitleDetermination of the mechanism of orotidine 5'-monophosphate decarboxylase by isotope effects.
[15]
PubMed ID11101287
JournalBiochemistry
Year2000
Volume39
Pages14728-38
AuthorsWarshel A, Strajbl M, Villa J, Florian J
TitleRemarkable rate enhancement of orotidine 5'-monophosphate decarboxylase is due to transition-state stabilization rather than to ground-state destabilization.
[16]
PubMed ID11114509
JournalCurr Opin Struct Biol
Year2000
Volume10
Pages711-8
AuthorsBegley TP, Appleby TC, Ealick SE
TitleThe structural basis for the remarkable catalytic proficiency of orotidine 5'-monophosphate decarboxylase.
[17]
CommentsX-ray crystallography
PubMed ID10681442
JournalProc Natl Acad Sci U S A
Year2000
Volume97
Pages2005-10
AuthorsAppleby TC, Kinsland C, Begley TP, Ealick SE
TitleThe crystal structure and mechanism of orotidine 5'-monophosphate decarboxylase.
Related PDB1dbt
[18]
CommentsX-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS).
Medline ID20160896
PubMed ID10681417
JournalProc Natl Acad Sci U S A
Year2000
Volume97
Pages2011-6
AuthorsMiller BG, Hassell AM, Wolfenden R, Milburn MV, Short SA
TitleAnatomy of a proficient enzyme: the structure of orotidine 5'-monophosphate decarboxylase in the presence and absence of a potential transition state analog.
Related PDB1dqw,1dqx
Related Swiss-protP03962
[19]
CommentsX-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS).
Medline ID20160897
PubMed ID10681441
JournalProc Natl Acad Sci U S A
Year2000
Volume97
Pages2017-22
AuthorsWu N, Mo Y, Gao J, Pai EF
TitleElectrostatic stress in catalysis: structure and mechanism of the enzyme orotidine monophosphate decarboxylase.
Related PDB1dv7,1dvj
Related Swiss-protO26232
[20]
PubMed ID11526316
JournalActa Crystallogr D Biol Crystallogr
Year2001
Volume57
Pages1251-9
AuthorsPoulsen JC, Harris P, Jensen KF, Larsen S
TitleSelenomethionine substitution of orotidine-5'-monophosphate decarboxylase causes a change in crystal contacts and space group.
Related PDB1jjk
[21]
PubMed ID11371183
JournalBiochemistry
Year2001
Volume40
Pages6227-32
AuthorsMiller BG, Butterfoss GL, Short SA, Wolfenden R
TitleRole of enzyme-ribofuranosyl contacts in the ground state and transition state for orotidine 5'-phosphate decarboxylase: a role for substrate destabilization?
[22]
PubMed ID11300698
JournalBioorg Chem
Year2001
Volume29
Pages96-106
AuthorsSmiley JA, Hay KM, Levison BS
TitleA reexamination of the substrate utilization of 2-thioorotidine-5'-monophosphate by yeast orotidine-5'-monophosphate decarboxylase.
[23]
PubMed ID11828434
JournalChembiochem
Year2001
Volume2
Pages113-8
AuthorsHouk KN, Lee JK, Tantillo DJ, Bahmanyar S, Hietbrink BN
TitleCrystal structures of orotidine monophosphate decarboxylase: does the structure reveal the mechanism of nature's most proficient enzyme?
[24]
PubMed ID11749542
JournalJ Am Chem Soc
Year2001
Volume123
Pages12837-48
AuthorsLee TS, Chong LT, Chodera JD, Kollman PA
TitleAn alternative explanation for the catalytic proficiency of orotidine 5'-phosphate decarboxylase.
[25]
PubMed ID11278904
JournalJ Biol Chem
Year2001
Volume276
Pages15174-6
AuthorsMiller BG, Snider MJ, Wolfenden R, Short SA
TitleDissecting a charged network at the active site of orotidine-5'-phosphate decarboxylase.
[26]
PubMed ID12045113
JournalAnnu Rev Biochem
Year2002
Volume71
Pages847-85
AuthorsMiller BG, Wolfenden R
TitleCatalytic proficiency: the unusual case of OMP decarboxylase.
[27]
PubMed ID11900527
JournalBiochemistry
Year2002
Volume41
Pages3861-9
AuthorsWise E, Yew WS, Babbitt PC, Gerlt JA, Rayment I
TitleHomologous (beta/alpha)8-barrel enzymes that catalyze unrelated reactions: orotidine 5'-monophosphate decarboxylase and 3-keto-L-gulonate 6-phosphate decarboxylase.
[28]
PubMed ID11900543
JournalBiochemistry
Year2002
Volume41
Pages4002-11
AuthorsWu N, Gillon W, Pai EF
TitleMapping the active site-ligand interactions of orotidine 5'-monophosphate decarboxylase by crystallography.
[29]
PubMed ID12430437
JournalChem Commun (Camb)
Year2002
Volume(20)
Pages2354-5
AuthorsKurinovich MA, Phillips LM, Sharma S, Lee JK
TitleThe gas phase proton affinity of uracil: measuring multiple basic sites and implications for the enzyme mechanism of orotidine 5'-monophosphate decarboxylase.
[30]
PubMed ID12011084
JournalJ Biol Chem
Year2002
Volume277
Pages28080-7
AuthorsWu N, Pai EF
TitleCrystal structures of inhibitor complexes reveal an alternate binding mode in orotidine-5'-monophosphate decarboxylase.
[31]
PubMed ID12054799
JournalJ Mol Biol
Year2002
Volume318
Pages1019-29
AuthorsHarris P, Poulsen JC, Jensen KF, Larsen S
TitleSubstrate binding induces domain movements in orotidine 5'-monophosphate decarboxylase.
Related PDB1l2u
[32]
PubMed ID12667491
JournalArch Biochem Biophys
Year2003
Volume412
Pages267-71
AuthorsSmiley JA, DelFraino BJ, Simpson BA
TitleHydrogen isotope tracing in the reaction of orotidine-5'-monophosphate decarboxylase.


createdupdated
2004-04-042009-02-26
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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