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Protein

Orotidine 5'-phosphate decarboxylase

Gene

pyrF

Organism
Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the decarboxylation of orotidine 5'-monophosphate (OMP) to uridine 5'-monophosphate (UMP).By similarity

Catalytic activityi

Orotidine 5'-phosphate = UMP + CO2.PROSITE-ProRule annotation

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei8 – 81SubstrateBy similarity
Binding sitei26 – 261SubstrateBy similarity
Active sitei54 – 541Proton donorPROSITE-ProRule annotation
Binding sitei106 – 1061SubstrateBy similarity
Binding sitei153 – 1531SubstrateBy similarity
Binding sitei161 – 1611SubstrateBy similarity
Binding sitei180 – 1801Substrate; via amide nitrogenBy similarity
Binding sitei181 – 1811SubstrateBy similarity

GO - Molecular functioni

  1. orotidine-5'-phosphate decarboxylase activity Source: UniProtKB-EC

GO - Biological processi

  1. 'de novo' pyrimidine nucleobase biosynthetic process Source: InterPro
  2. 'de novo' UMP biosynthetic process Source: UniProtKB-UniPathway
Complete GO annotation...

Keywords - Molecular functioni

Decarboxylase, Lyase

Keywords - Biological processi

Pyrimidine biosynthesis

Enzyme and pathway databases

UniPathwayiUPA00070; UER00120.

Names & Taxonomyi

Protein namesi
Recommended name:
Orotidine 5'-phosphate decarboxylase (EC:4.1.1.23)
Alternative name(s):
OMP decarboxylase
Short name:
OMPDCase
Short name:
OMPdecase
Gene namesi
Name:pyrF
Ordered Locus Names:TM_0332
OrganismiThermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
Taxonomic identifieri243274 [NCBI]
Taxonomic lineageiBacteriaThermotogaeThermotogalesThermotogaceaeThermotoga
ProteomesiUP000008183 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 201201Orotidine 5'-phosphate decarboxylasePRO_0000134595Add
BLAST

Interactioni

Subunit structurei

Homodimer.1 Publication

Protein-protein interaction databases

STRINGi243274.TM0332.

Structurei

Secondary structure

1
201
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi2 – 65Combined sources
Beta strandi9 – 113Combined sources
Helixi12 – 198Combined sources
Beta strandi23 – 275Combined sources
Helixi29 – 324Combined sources
Helixi37 – 437Combined sources
Turni44 – 463Combined sources
Beta strandi48 – 558Combined sources
Helixi59 – 6911Combined sources
Beta strandi74 – 807Combined sources
Helixi81 – 833Combined sources
Helixi85 – 9410Combined sources
Beta strandi96 – 1027Combined sources
Helixi112 – 12413Combined sources
Beta strandi128 – 1303Combined sources
Helixi133 – 1397Combined sources
Turni140 – 1423Combined sources
Beta strandi147 – 1493Combined sources
Helixi167 – 1704Combined sources
Turni171 – 1733Combined sources
Beta strandi175 – 1806Combined sources
Helixi181 – 1844Combined sources
Helixi189 – 1968Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1VQTX-ray2.00A1-201[»]
ProteinModelPortaliQ9WYG7.
SMRiQ9WYG7. Positions 1-198.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9WYG7.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni52 – 6110Substrate bindingBy similarity

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG0284.
InParanoidiQ9WYG7.
KOiK01591.
OMAiIVGFTVH.
OrthoDBiEOG6N6815.

Family and domain databases

Gene3Di3.20.20.70. 1 hit.
InterProiIPR013785. Aldolase_TIM.
IPR014732. OMPdecase.
IPR018089. OMPdecase_AS.
IPR001754. OMPdeCOase_dom.
IPR011060. RibuloseP-bd_barrel.
[Graphical view]
PfamiPF00215. OMPdecase. 1 hit.
[Graphical view]
SMARTiSM00934. OMPdecase. 1 hit.
[Graphical view]
SUPFAMiSSF51366. SSF51366. 1 hit.
TIGRFAMsiTIGR01740. pyrF. 1 hit.
PROSITEiPS00156. OMPDECASE. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q9WYG7-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTPVLSLDME DPIRFIDENG SFEVVKVGHN LAIHGKKIFD ELAKRNLKII
60 70 80 90 100
LDLKFCDIPS TVERSIKSWD HPAIIGFTVH SCAGYESVER ALSATDKHVF
110 120 130 140 150
VVVKLTSMEG SLEDYMDRIE KLNKLGCDFV LPGPWAKALR EKIKGKILVP
160 170 180 190 200
GIRMEVKADD QKDVVTLEEM KGIANFAVLG REIYLSENPR EKIKRIKEMR

L
Length:201
Mass (Da):22,809
Last modified:November 1, 1999 - v1
Checksum:i4C2FAD77302F206D
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000512 Genomic DNA. Translation: AAD35419.1.
PIRiF72390.
RefSeqiNP_228143.1. NC_000853.1.
YP_007976680.1. NC_021214.1.
YP_008990695.1. NC_023151.1.

Genome annotation databases

EnsemblBacteriaiAAD35419; AAD35419; TM_0332.
GeneIDi897284.
KEGGitma:TM0332.
tmi:THEMA_03060.
PATRICi23935545. VBITheMar51294_0337.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000512 Genomic DNA. Translation: AAD35419.1.
PIRiF72390.
RefSeqiNP_228143.1. NC_000853.1.
YP_007976680.1. NC_021214.1.
YP_008990695.1. NC_023151.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1VQTX-ray2.00A1-201[»]
ProteinModelPortaliQ9WYG7.
SMRiQ9WYG7. Positions 1-198.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi243274.TM0332.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAD35419; AAD35419; TM_0332.
GeneIDi897284.
KEGGitma:TM0332.
tmi:THEMA_03060.
PATRICi23935545. VBITheMar51294_0337.

Phylogenomic databases

eggNOGiCOG0284.
InParanoidiQ9WYG7.
KOiK01591.
OMAiIVGFTVH.
OrthoDBiEOG6N6815.

Enzyme and pathway databases

UniPathwayiUPA00070; UER00120.

Miscellaneous databases

EvolutionaryTraceiQ9WYG7.

Family and domain databases

Gene3Di3.20.20.70. 1 hit.
InterProiIPR013785. Aldolase_TIM.
IPR014732. OMPdecase.
IPR018089. OMPdecase_AS.
IPR001754. OMPdeCOase_dom.
IPR011060. RibuloseP-bd_barrel.
[Graphical view]
PfamiPF00215. OMPdecase. 1 hit.
[Graphical view]
SMARTiSM00934. OMPdecase. 1 hit.
[Graphical view]
SUPFAMiSSF51366. SSF51366. 1 hit.
TIGRFAMsiTIGR01740. pyrF. 1 hit.
PROSITEiPS00156. OMPDECASE. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099.
  2. "Crystal Structure of orotidine 5'-phosphate decarboxylase (TM0332) from Thermotoga maritima at 2.00 A resolution."
    Joint center for structural genomics (JCSG)
    Submitted (JAN-2005) to the PDB data bank
    Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS), SUBUNIT.

Entry informationi

Entry nameiPYRF_THEMA
AccessioniPrimary (citable) accession number: Q9WYG7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: November 1, 1999
Last modified: April 1, 2015
This is version 110 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.