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Protein

Orotidine 5'-phosphate decarboxylase

Gene

pyrF

Organism
Geobacter bemidjiensis (strain Bem / ATCC BAA-1014 / DSM 16622)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

Functioni

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

Catalytic activityi

Orotidine 5'-phosphate = UMP + CO2.UniRule annotation

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei15 – 151SubstrateUniRule annotation
Binding sitei37 – 371SubstrateUniRule annotation
Active sitei66 – 661Proton donorUniRule annotation
Binding sitei127 – 1271SubstrateUniRule annotation
Binding sitei188 – 1881SubstrateUniRule annotation
Binding sitei197 – 1971SubstrateUniRule annotation
Binding sitei217 – 2171Substrate; via amide nitrogenUniRule annotation
Binding sitei218 – 2181SubstrateUniRule annotation

GO - Molecular functioni

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

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

BioCyciGBEM404380:GHFR-2944-MONOMER.
UniPathwayiUPA00070; UER00120.

Names & Taxonomyi

Protein namesi
Recommended name:
Orotidine 5'-phosphate decarboxylaseUniRule annotation (EC:4.1.1.23UniRule annotation)
Alternative name(s):
OMP decarboxylaseUniRule annotation
Short name:
OMPDCaseUniRule annotation
Short name:
OMPdecaseUniRule annotation
Gene namesi
Name:pyrFUniRule annotation
Ordered Locus Names:Gbem_2890
OrganismiGeobacter bemidjiensis (strain Bem / ATCC BAA-1014 / DSM 16622)
Taxonomic identifieri404380 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaDeltaproteobacteriaDesulfuromonadalesGeobacteraceaeGeobacter
ProteomesiUP000008825 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 240240Orotidine 5'-phosphate decarboxylasePRO_1000138530Add
BLAST

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi404380.Gbem_2890.

Structurei

3D structure databases

ProteinModelPortaliB5EIT8.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni64 – 7310Substrate bindingUniRule annotation

Sequence similaritiesi

Belongs to the OMP decarboxylase family. Type 1 subfamily.UniRule annotation

Phylogenomic databases

eggNOGiCOG0284.
HOGENOMiHOG000226071.
KOiK01591.
OMAiNFKIFLD.
OrthoDBiEOG6N6815.

Family and domain databases

Gene3Di3.20.20.70. 1 hit.
HAMAPiMF_01200_B. OMPdecase_type1_B.
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.

B5EIT8-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTREEAIKKI IFAMDVKEFS DVQYWAELLS QHVGMFKVGK QLYTACGPAA
60 70 80 90 100
VRMIQKCGGE VFLDLKYHDI PNTVAMATLE AANLGVQLCD LHAMGGYEMM
110 120 130 140 150
NKTMETLDKN FSGCTARPKV LAITVLTSSN EETLRGIGIE LPVPEMVVKL
160 170 180 190 200
AKLAKSAGVD GVVASPQEVE LIREACGKDF LVVTPGVRPS FASADDQKRI
210 220 230 240
MSPAEAVKAG ADYLVIGRPI AAAQSPVEAA QKIVDEIVAG
Length:240
Mass (Da):25,788
Last modified:October 14, 2008 - v1
Checksum:i7D0D6C510EE45A12
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001124 Genomic DNA. Translation: ACH39893.1.
RefSeqiYP_002139689.1. NC_011146.1.

Genome annotation databases

EnsemblBacteriaiACH39893; ACH39893; Gbem_2890.
KEGGigbm:Gbem_2890.
PATRICi21989446. VBIGeoBem56306_2836.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001124 Genomic DNA. Translation: ACH39893.1.
RefSeqiYP_002139689.1. NC_011146.1.

3D structure databases

ProteinModelPortaliB5EIT8.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi404380.Gbem_2890.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiACH39893; ACH39893; Gbem_2890.
KEGGigbm:Gbem_2890.
PATRICi21989446. VBIGeoBem56306_2836.

Phylogenomic databases

eggNOGiCOG0284.
HOGENOMiHOG000226071.
KOiK01591.
OMAiNFKIFLD.
OrthoDBiEOG6N6815.

Enzyme and pathway databases

UniPathwayiUPA00070; UER00120.
BioCyciGBEM404380:GHFR-2944-MONOMER.

Family and domain databases

Gene3Di3.20.20.70. 1 hit.
HAMAPiMF_01200_B. OMPdecase_type1_B.
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

  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: Bem / ATCC BAA-1014 / DSM 16622.

Entry informationi

Entry nameiPYRF_GEOBB
AccessioniPrimary (citable) accession number: B5EIT8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 14, 2009
Last sequence update: October 14, 2008
Last modified: April 1, 2015
This is version 43 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

Complete proteome, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. 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.