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Protein

Orotidine 5'-phosphate decarboxylase

Gene

pyrF

Organism
Lactobacillus acidophilus (strain ATCC 700396 / NCK56 / N2 / NCFM)
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 sitei10 – 101SubstrateUniRule annotation
Binding sitei33 – 331SubstrateUniRule annotation
Active sitei62 – 621Proton donorUniRule annotation
Binding sitei123 – 1231SubstrateUniRule annotation
Binding sitei185 – 1851SubstrateUniRule annotation
Binding sitei194 – 1941SubstrateUniRule annotation
Binding sitei214 – 2141Substrate; via amide nitrogenUniRule annotation
Binding sitei215 – 2151SubstrateUniRule 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

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:LBA1386
OrganismiLactobacillus acidophilus (strain ATCC 700396 / NCK56 / N2 / NCFM)
Taxonomic identifieri272621 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliLactobacillalesLactobacillaceaeLactobacillus
ProteomesiUP000006381 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 235235Orotidine 5'-phosphate decarboxylasePRO_0000241868Add
BLAST

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi272621.LBA1386.

Structurei

Secondary structure

1
235
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi5 – 84Combined sources
Helixi14 – 229Combined sources
Helixi27 – 293Combined sources
Beta strandi31 – 344Combined sources
Helixi36 – 427Combined sources
Helixi44 – 529Combined sources
Beta strandi56 – 638Combined sources
Helixi67 – 7812Combined sources
Turni79 – 813Combined sources
Beta strandi83 – 886Combined sources
Helixi89 – 913Combined sources
Helixi93 – 10614Combined sources
Beta strandi115 – 1195Combined sources
Helixi127 – 1326Combined sources
Beta strandi136 – 1383Combined sources
Helixi140 – 15314Combined sources
Beta strandi158 – 1603Combined sources
Helixi163 – 1653Combined sources
Helixi166 – 1738Combined sources
Beta strandi175 – 1817Combined sources
Helixi200 – 2056Combined sources
Beta strandi209 – 2135Combined sources
Helixi215 – 2184Combined sources
Beta strandi220 – 2223Combined sources
Helixi223 – 23412Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3TFXX-ray2.19A/B1-235[»]
ProteinModelPortaliQ5FJB3.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni60 – 6910Substrate 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.

Q5FJB3-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MDRPVIVALD LDNEEQLNKI LSKLGDPHDV FVKVGMELFY NAGIDVIKKL
60 70 80 90 100
TQQGYKIFLD LKMHDIPNTV YNGAKALAKL GITFTTVHAL GGSQMIKSAK
110 120 130 140 150
DGLIAGTPAG HSVPKLLAVT ELTSISDDVL RNEQNCRLPM AEQVLSLAKM
160 170 180 190 200
AKHSGADGVI CSPLEVKKLH ENIGDDFLYV TPGIRPAGNA KDDQSRVATP
210 220 230
KMAKEWGSSA IVVGRPITLA SDPKAAYEAI KKEFN
Length:235
Mass (Da):25,404
Last modified:March 1, 2005 - v1
Checksum:i892076F9C45D7B1F
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000033 Genomic DNA. Translation: AAV43211.1.
RefSeqiYP_194242.1. NC_006814.3.

Genome annotation databases

EnsemblBacteriaiAAV43211; AAV43211; LBA1386.
GeneIDi3252592.
KEGGilac:LBA1386.
PATRICi22197796. VBILacAci7974_1311.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000033 Genomic DNA. Translation: AAV43211.1.
RefSeqiYP_194242.1. NC_006814.3.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3TFXX-ray2.19A/B1-235[»]
ProteinModelPortaliQ5FJB3.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi272621.LBA1386.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAV43211; AAV43211; LBA1386.
GeneIDi3252592.
KEGGilac:LBA1386.
PATRICi22197796. VBILacAci7974_1311.

Phylogenomic databases

eggNOGiCOG0284.
HOGENOMiHOG000226071.
KOiK01591.
OMAiNFKIFLD.
OrthoDBiEOG6N6815.

Enzyme and pathway databases

UniPathwayiUPA00070; UER00120.

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: ATCC 700396 / NCK56 / N2 / NCFM.

Entry informationi

Entry nameiPYRF_LACAC
AccessioniPrimary (citable) accession number: Q5FJB3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 27, 2006
Last sequence update: March 1, 2005
Last modified: January 7, 2015
This is version 65 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

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.