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Q2JPF1

- PYRF_SYNJB

UniProt

Q2JPF1 - PYRF_SYNJB

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Protein

Orotidine 5'-phosphate decarboxylase

Gene

pyrF

Organism
Synechococcus sp. (strain JA-2-3B'a(2-13)) (Cyanobacteria bacterium Yellowstone B-Prime)
Status
Reviewed - 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 sitei11 – 111SubstrateUniRule annotation
Binding sitei32 – 321SubstrateUniRule annotation
Active sitei61 – 611Proton donorUniRule annotation
Binding sitei116 – 1161SubstrateUniRule annotation
Binding sitei178 – 1781SubstrateUniRule annotation
Binding sitei191 – 1911SubstrateUniRule annotation
Binding sitei211 – 2111Substrate; via amide nitrogenUniRule annotation
Binding sitei212 – 2121SubstrateUniRule 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

BioCyciSSP321332:GH1B-343-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:CYB_0343
OrganismiSynechococcus sp. (strain JA-2-3B'a(2-13)) (Cyanobacteria bacterium Yellowstone B-Prime)
Taxonomic identifieri321332 [NCBI]
Taxonomic lineageiBacteriaCyanobacteriaOscillatoriophycideaeChroococcalesSynechococcus
ProteomesiUP000001938: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 235235Orotidine 5'-phosphate decarboxylasePRO_0000241919Add
BLAST

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi321332.CYB_0343.

Structurei

3D structure databases

ProteinModelPortaliQ2JPF1.
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.
HOGENOMiHOG000226070.
KOiK01591.
OMAiDIPNTMR.
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.

Q2JPF1-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MKGDRLIVAL DTPSQEQALE WVDSLPQVLW WKVGLELFTA AGSSILQALK
60 70 80 90 100
ERGKRIFLDL KLHDIPHTVG RATEVAVGYG VDLLTVHAAG GSAMLRSAVA
110 120 130 140 150
AAQGSSCRLL AVTLLTSISP PQVRQELGIE MDPADYVLHL ARLAQAQGFT
160 170 180 190 200
GLVCSPQEVS RLRQALGPEV LLVTPGIRLG QAKAGDGDED QQRICTPDEA
210 220 230
LRAGADYLVV GRPITASPDP VAALRRFQAL WDAAS
Length:235
Mass (Da):25,103
Last modified:March 7, 2006 - v1
Checksum:iB1DAB5181BFC356F
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000240 Genomic DNA. Translation: ABD01339.1.
RefSeqiWP_011432008.1. NC_007776.1.
YP_476602.1. NC_007776.1.

Genome annotation databases

EnsemblBacteriaiABD01339; ABD01339; CYB_0343.
GeneIDi3901284.
KEGGicyb:CYB_0343.
PATRICi23802976. VBISynSp29577_0354.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000240 Genomic DNA. Translation: ABD01339.1 .
RefSeqi WP_011432008.1. NC_007776.1.
YP_476602.1. NC_007776.1.

3D structure databases

ProteinModelPortali Q2JPF1.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 321332.CYB_0343.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai ABD01339 ; ABD01339 ; CYB_0343 .
GeneIDi 3901284.
KEGGi cyb:CYB_0343.
PATRICi 23802976. VBISynSp29577_0354.

Phylogenomic databases

eggNOGi COG0284.
HOGENOMi HOG000226070.
KOi K01591.
OMAi DIPNTMR.
OrthoDBi EOG6N6815.

Enzyme and pathway databases

UniPathwayi UPA00070 ; UER00120 .
BioCyci SSP321332:GH1B-343-MONOMER.

Family and domain databases

Gene3Di 3.20.20.70. 1 hit.
HAMAPi MF_01200_B. OMPdecase_type1_B.
InterProi IPR013785. Aldolase_TIM.
IPR014732. OMPdecase.
IPR018089. OMPdecase_AS.
IPR001754. OMPdeCOase_dom.
IPR011060. RibuloseP-bd_barrel.
[Graphical view ]
Pfami PF00215. OMPdecase. 1 hit.
[Graphical view ]
SMARTi SM00934. OMPdecase. 1 hit.
[Graphical view ]
SUPFAMi SSF51366. SSF51366. 1 hit.
TIGRFAMsi TIGR01740. pyrF. 1 hit.
PROSITEi PS00156. OMPDECASE. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

  1. "Population level functional diversity in a microbial community revealed by comparative genomic and metagenomic analyses."
    Bhaya D., Grossman A.R., Steunou A.-S., Khuri N., Cohan F.M., Hamamura N., Melendrez M.C., Bateson M.M., Ward D.M., Heidelberg J.F.
    ISME J. 1:703-713(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: JA-2-3B'a(2-13).

Entry informationi

Entry nameiPYRF_SYNJB
AccessioniPrimary (citable) accession number: Q2JPF1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 27, 2006
Last sequence update: March 7, 2006
Last modified: October 1, 2014
This is version 59 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