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B3DVI6

- PYRF_METI4

UniProt

B3DVI6 - PYRF_METI4

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Protein

Orotidine 5'-phosphate decarboxylase

Gene

pyrF

Organism
Methylacidiphilum infernorum (isolate V4) (Methylokorus infernorum (strain V4))
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 sitei10 – 101SubstrateUniRule annotation
Binding sitei32 – 321SubstrateUniRule annotation
Active sitei61 – 611Proton donorUniRule annotation
Binding sitei116 – 1161SubstrateUniRule annotation
Binding sitei177 – 1771SubstrateUniRule annotation
Binding sitei186 – 1861SubstrateUniRule annotation
Binding sitei206 – 2061Substrate; via amide nitrogenUniRule annotation
Binding sitei207 – 2071SubstrateUniRule 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

BioCyciMINF481448:GJEI-1310-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:Minf_1285
OrganismiMethylacidiphilum infernorum (isolate V4) (Methylokorus infernorum (strain V4))
Taxonomic identifieri481448 [NCBI]
Taxonomic lineageiBacteriaVerrucomicrobiaunclassified VerrucomicrobiaMethylacidiphilalesMethylacidiphilaceaeMethylacidiphilum
ProteomesiUP000009149: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 230230Orotidine 5'-phosphate decarboxylasePRO_1000164576Add
BLAST

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi481448.Minf_1285.

Structurei

3D structure databases

ProteinModelPortaliB3DVI6.
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.
OMAiGANGDTN.
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.

B3DVI6-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MDLKPIVALD LPDPSEALKL VHLLRPHIDF FKVGSQLFLA GGTDIIRRII
60 70 80 90 100
DCGADVFLDL KFHDIPRTVF RAVTEVVKLK VKFTTVHILG GREMLKEALE
110 120 130 140 150
ASAGSDTEIL GVTVLTSMDD RGLESIGIAH AVEEEVLLLA SMALEVGLRG
160 170 180 190 200
IVCSGKELPL LGKLKKRASI LVVPGIRWRG AAAYDQKRII EPGEAKKGGA
210 220 230
THVVVGRPIL EAHDKVGLVQ KLLCELNAIN
Length:230
Mass (Da):24,929
Last modified:July 22, 2008 - v1
Checksum:iAE167409AB580D5B
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000975 Genomic DNA. Translation: ACD83339.1.
RefSeqiYP_001939937.1. NC_010794.1.

Genome annotation databases

EnsemblBacteriaiACD83339; ACD83339; Minf_1285.
GeneIDi6352220.
KEGGimin:Minf_1285.
PATRICi22491713. VBIMetInf111569_1343.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000975 Genomic DNA. Translation: ACD83339.1 .
RefSeqi YP_001939937.1. NC_010794.1.

3D structure databases

ProteinModelPortali B3DVI6.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 481448.Minf_1285.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai ACD83339 ; ACD83339 ; Minf_1285 .
GeneIDi 6352220.
KEGGi min:Minf_1285.
PATRICi 22491713. VBIMetInf111569_1343.

Phylogenomic databases

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

Enzyme and pathway databases

UniPathwayi UPA00070 ; UER00120 .
BioCyci MINF481448:GJEI-1310-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. "Complete genome sequence of the extremely acidophilic methanotroph isolate V4, Methylacidiphilum infernorum, a representative of the bacterial phylum Verrucomicrobia."
    Hou S., Makarova K.S., Saw J.H., Senin P., Ly B.V., Zhou Z., Ren Y., Wang J., Galperin M.Y., Omelchenko M.V., Wolf Y.I., Yutin N., Koonin E.V., Stott M.B., Mountain B.W., Crowe M.A., Smirnova A.V., Dunfield P.F.
    , Feng L., Wang L., Alam M.
    Biol. Direct 3:26-26(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: Isolate V4.

Entry informationi

Entry nameiPYRF_METI4
AccessioniPrimary (citable) accession number: B3DVI6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 28, 2009
Last sequence update: July 22, 2008
Last modified: October 1, 2014
This is version 44 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