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Protein

Orotidine 5'-phosphate decarboxylase

Gene

pyrF

Organism
Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126)
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).UniRule annotation

Catalytic activityi

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

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei9 – 91SubstrateUniRule annotation
Binding sitei31 – 311SubstrateUniRule annotation
Active sitei59 – 591Proton donorUniRule annotation
Binding sitei114 – 1141SubstrateUniRule annotation
Binding sitei187 – 1871Substrate; via amide nitrogenUniRule annotation
Binding sitei188 – 1881SubstrateUniRule 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

BioCyciAFUL224325:GJBC-951-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:AF_0929
OrganismiArchaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126)
Taxonomic identifieri224325 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaArchaeoglobiArchaeoglobalesArchaeoglobaceaeArchaeoglobus
ProteomesiUP000002199 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 209209Orotidine 5'-phosphate decarboxylasePRO_0000134608Add
BLAST

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi224325.AF0929.

Structurei

Secondary structure

1
209
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi3 – 75Combined sources
Helixi13 – 2311Combined sources
Helixi24 – 263Combined sources
Beta strandi28 – 336Combined sources
Helixi34 – 407Combined sources
Helixi44 – 496Combined sources
Beta strandi54 – 607Combined sources
Helixi64 – 7613Combined sources
Beta strandi80 – 856Combined sources
Helixi86 – 883Combined sources
Helixi90 – 10213Combined sources
Beta strandi106 – 1105Combined sources
Helixi116 – 1194Combined sources
Helixi122 – 13615Combined sources
Beta strandi140 – 1423Combined sources
Helixi148 – 15811Combined sources
Beta strandi162 – 1654Combined sources
Beta strandi169 – 1713Combined sources
Helixi175 – 1795Combined sources
Beta strandi182 – 1876Combined sources
Helixi188 – 1914Combined sources
Beta strandi192 – 1943Combined sources
Helixi196 – 20712Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4MUZX-ray1.39A/B1-209[»]
4N2YX-ray1.55A/B/C/D1-209[»]
ProteinModelPortaliO29333.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni57 – 6610Substrate bindingUniRule annotation
Regioni166 – 17611Substrate bindingUniRule annotationAdd
BLAST

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiCOG0284.
KOiK01591.
OMAiVIMVTEM.

Family and domain databases

Gene3Di3.20.20.70. 1 hit.
HAMAPiMF_01200_A. OMPdecase_type1_A.
InterProiIPR013785. Aldolase_TIM.
IPR014732. OMPdecase.
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.

Sequencei

Sequence statusi: Complete.

O29333-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKQLILALDV MDGEKAMEIA KKVAEHVDRI KVNYPLVLSA GVGIMKRLSE
60 70 80 90 100
IKPVIADFKI ADVPYTSSLI ARIAFENSAE SVIVHGFVGS DTLREVCRVA
110 120 130 140 150
EEFGGKVYAV TELSSPGGEE FMSAVSLKIV EKAKEAGCHG LIAPSTRIER
160 170 180 190 200
LREIRKAAGD MEILCPGIGA QKGSIEAVKY ADGIIVGRGI YASGNPAEEA

RKLRRVLKI
Length:209
Mass (Da):22,538
Last modified:January 22, 2002 - v2
Checksum:iC6CBB39E9C105B66
GO

Sequence cautioni

The sequence AAB90309.1 differs from that shown. Reason: Erroneous initiation. Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000782 Genomic DNA. Translation: AAB90309.1. Different initiation.
PIRiA69366.
RefSeqiNP_069762.1. NC_000917.1.

Genome annotation databases

EnsemblBacteriaiAAB90309; AAB90309; AF_0929.
GeneIDi1484152.
KEGGiafu:AF0929.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000782 Genomic DNA. Translation: AAB90309.1. Different initiation.
PIRiA69366.
RefSeqiNP_069762.1. NC_000917.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4MUZX-ray1.39A/B1-209[»]
4N2YX-ray1.55A/B/C/D1-209[»]
ProteinModelPortaliO29333.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi224325.AF0929.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAB90309; AAB90309; AF_0929.
GeneIDi1484152.
KEGGiafu:AF0929.

Phylogenomic databases

eggNOGiCOG0284.
KOiK01591.
OMAiVIMVTEM.

Enzyme and pathway databases

UniPathwayiUPA00070; UER00120.
BioCyciAFUL224325:GJBC-951-MONOMER.

Family and domain databases

Gene3Di3.20.20.70. 1 hit.
HAMAPiMF_01200_A. OMPdecase_type1_A.
InterProiIPR013785. Aldolase_TIM.
IPR014732. OMPdecase.
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.
ProtoNetiSearch...

Publicationsi

  1. "The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus."
    Klenk H.-P., Clayton R.A., Tomb J.-F., White O., Nelson K.E., Ketchum K.A., Dodson R.J., Gwinn M.L., Hickey E.K., Peterson J.D., Richardson D.L., Kerlavage A.R., Graham D.E., Kyrpides N.C., Fleischmann R.D., Quackenbush J., Lee N.H., Sutton G.G.
    , Gill S.R., Kirkness E.F., Dougherty B.A., McKenney K., Adams M.D., Loftus B.J., Peterson S.N., Reich C.I., McNeil L.K., Badger J.H., Glodek A., Zhou L., Overbeek R., Gocayne J.D., Weidman J.F., McDonald L.A., Utterback T.R., Cotton M.D., Spriggs T., Artiach P., Kaine B.P., Sykes S.M., Sadow P.W., D'Andrea K.P., Bowman C., Fujii C., Garland S.A., Mason T.M., Olsen G.J., Fraser C.M., Smith H.O., Woese C.R., Venter J.C.
    Nature 390:364-370(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126.

Entry informationi

Entry nameiPYRF_ARCFU
AccessioniPrimary (citable) accession number: O29333
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 29, 2000
Last sequence update: January 22, 2002
Last modified: January 6, 2015
This is version 95 of the entry and version 2 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.