Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

Orotidine 5'-phosphate decarboxylase

Gene

pyrF

Organism
Helicobacter pylori (strain Shi470)
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

Pathway:iUMP biosynthesis via de novo pathway

This protein is involved in step 2 of the subpathway that synthesizes UMP from orotate.UniRule annotation
Proteins known to be involved in the 2 steps of the subpathway in this organism are:
  1. Orotate phosphoribosyltransferase (pyrE)
  2. Orotidine 5'-phosphate decarboxylase (pyrF)
This subpathway is part of the pathway UMP biosynthesis via de novo pathway, which is itself part of Pyrimidine metabolism.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes UMP from orotate, the pathway UMP biosynthesis via de novo pathway and in Pyrimidine metabolism.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei8 – 81SubstrateUniRule annotation
Binding sitei30 – 301SubstrateUniRule annotation
Active sitei61 – 611Proton donorUniRule annotation
Binding sitei118 – 1181SubstrateUniRule annotation
Binding sitei178 – 1781SubstrateUniRule annotation
Binding sitei187 – 1871SubstrateUniRule annotation
Binding sitei207 – 2071Substrate; via amide nitrogenUniRule annotation
Binding sitei208 – 2081SubstrateUniRule annotation

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Decarboxylase, Lyase

Keywords - Biological processi

Pyrimidine biosynthesis

Enzyme and pathway databases

BioCyciHPYL512562:GHHZ-5-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:HPSH_00025
OrganismiHelicobacter pylori (strain Shi470)
Taxonomic identifieri512562 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaEpsilonproteobacteriaCampylobacteralesHelicobacteraceaeHelicobacter

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 227227Orotidine 5'-phosphate decarboxylasePRO_1000138534Add
BLAST

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Structurei

3D structure databases

ProteinModelPortaliB2UW09.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni59 – 6810Substrate 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.

B2UW09-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MQLCVALDLE KKEDNLSLLQ ELKGLDLWAK VGLRSFIRDG AVFLDEIRKI
60 70 80 90 100
DGNFKIFLDL KLYDIPYTMA NAALECAKLE VDMLTVHLSS AKSALTILMQ
110 120 130 140 150
RLNALKKRPL IMGVSALTSF SEEEFLSVYN APLKTQAIKL SVMGKESGID
160 170 180 190 200
GVVCSVFESL AIKEALGKDF LTLTPGIRLN KNDKEDQERV ANAKEAKQNL
210 220
SDFIVVGRPI YQAKEPREVV LELLKDC
Length:227
Mass (Da):25,337
Last modified:July 1, 2008 - v1
Checksum:iC81FAEDBF0E50738
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001072 Genomic DNA. Translation: ACD47474.1.
RefSeqiWP_001175355.1. NC_010698.2.

Genome annotation databases

EnsemblBacteriaiACD47474; ACD47474; HPSH_00025.
KEGGihps:HPSH_00025.
PATRICi20611361. VBIHelPyl23559_0005.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001072 Genomic DNA. Translation: ACD47474.1.
RefSeqiWP_001175355.1. NC_010698.2.

3D structure databases

ProteinModelPortaliB2UW09.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiACD47474; ACD47474; HPSH_00025.
KEGGihps:HPSH_00025.
PATRICi20611361. VBIHelPyl23559_0005.

Phylogenomic databases

eggNOGiCOG0284.
HOGENOMiHOG000226071.
KOiK01591.
OMAiNFKIFLD.
OrthoDBiEOG6N6815.

Enzyme and pathway databases

UniPathwayiUPA00070; UER00120.
BioCyciHPYL512562:GHHZ-5-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. "Genome sequence of Helicobacter pylori from the remote Amazon: traces of Asian ancestry of the first Americans."
    Kersulyte D., Kalia A., Gilman R.H., Berg D.E.
    Submitted (MAY-2008) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: Shi470.

Entry informationi

Entry nameiPYRF_HELPS
AccessioniPrimary (citable) accession number: B2UW09
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 14, 2009
Last sequence update: July 1, 2008
Last modified: July 22, 2015
This is version 48 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

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.