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P08244

- PYRF_ECOLI

UniProt

P08244 - PYRF_ECOLI

Protein

Orotidine 5'-phosphate decarboxylase

Gene

pyrF

Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 131 (01 Oct 2014)
      Sequence version 1 (01 Aug 1988)
      Previous versions | rss
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    Functioni

    Catalyzes the decarboxylation of orotidine 5'-monophosphate (OMP) to uridine 5'-monophosphate (UMP).

    Catalytic activityi

    Orotidine 5'-phosphate = UMP + CO2.

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei22 – 221Substrate
    Binding sitei44 – 441Substrate
    Active sitei73 – 731Proton donor
    Binding sitei131 – 1311Substrate
    Binding sitei192 – 1921Substrate
    Binding sitei201 – 2011Substrate
    Binding sitei221 – 2211Substrate; via amide nitrogen
    Binding sitei222 – 2221Substrate

    GO - Molecular functioni

    1. carboxy-lyase activity Source: EcoliWiki
    2. orotidine-5'-phosphate decarboxylase activity Source: EcoCyc
    3. protein binding Source: IntAct

    GO - Biological processi

    1. 'de novo' pyrimidine nucleobase biosynthetic process Source: EcoCyc
    2. 'de novo' UMP biosynthetic process Source: UniProtKB-UniPathway
    3. nucleobase-containing small molecule interconversion Source: EcoliWiki

    Keywords - Molecular functioni

    Decarboxylase, Lyase

    Keywords - Biological processi

    Pyrimidine biosynthesis

    Enzyme and pathway databases

    BioCyciEcoCyc:OROTPDECARB-MONOMER.
    ECOL316407:JW1273-MONOMER.
    MetaCyc:OROTPDECARB-MONOMER.
    UniPathwayiUPA00070; UER00120.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Orotidine 5'-phosphate decarboxylase (EC:4.1.1.23)
    Alternative name(s):
    OMP decarboxylase
    Short name:
    OMPDCase
    Short name:
    OMPdecase
    Gene namesi
    Name:pyrF
    Ordered Locus Names:b1281, JW1273
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

    Organism-specific databases

    EcoGeneiEG10809. pyrF.

    Subcellular locationi

    GO - Cellular componenti

    1. cytoplasm Source: EcoliWiki

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 245245Orotidine 5'-phosphate decarboxylasePRO_0000134539Add
    BLAST

    Proteomic databases

    PaxDbiP08244.
    PRIDEiP08244.

    2D gel databases

    SWISS-2DPAGEP08244.

    Expressioni

    Gene expression databases

    GenevestigatoriP08244.

    Interactioni

    Subunit structurei

    Homodimer.3 Publications

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    ribAP0A7I72EBI-1123202,EBI-1123314

    Protein-protein interaction databases

    IntActiP08244. 4 interactions.
    STRINGi511145.b1281.

    Structurei

    Secondary structure

    1
    245
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi17 – 215
    Helixi26 – 338
    Turni38 – 403
    Beta strandi42 – 465
    Helixi47 – 6317
    Beta strandi68 – 747
    Helixi78 – 9114
    Beta strandi94 – 996
    Helixi100 – 1023
    Helixi104 – 1129
    Helixi113 – 1208
    Beta strandi123 – 1275
    Helixi135 – 1395
    Turni140 – 1423
    Helixi147 – 16014
    Beta strandi164 – 1674
    Helixi170 – 1723
    Helixi173 – 1808
    Beta strandi182 – 1887
    Helixi207 – 2126
    Beta strandi216 – 2205
    Helixi222 – 2254
    Beta strandi227 – 2293
    Helixi230 – 24011

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1EIXX-ray2.50A/B/C/D1-245[»]
    1JJKX-ray3.00A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P1-245[»]
    1L2UX-ray2.50A/B1-245[»]
    ProteinModelPortaliP08244.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP08244.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni71 – 8010Substrate binding

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiCOG0284.
    HOGENOMiHOG000226071.
    KOiK01591.
    OMAiRPITQSA.
    OrthoDBiEOG6N6815.
    PhylomeDBiP08244.

    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.

    P08244-1 [UniParc]FASTAAdd to Basket

    « Hide

    MTLTASSSSR AVTNSPVVVA LDYHNRDDAL AFVDKIDPRD CRLKVGKEMF    50
    TLFGPQFVRE LQQRGFDIFL DLKFHDIPNT AAHAVAAAAD LGVWMVNVHA 100
    SGGARMMTAA REALVPFGKD APLLIAVTVL TSMEASDLVD LGMTLSPADY 150
    AERLAALTQK CGLDGVVCSA QEAVRFKQVF GQEFKLVTPG IRPQGSEAGD 200
    QRRIMTPEQA LSAGVDYMVI GRPVTQSVDP AQTLKAINAS LQRSA 245
    Length:245
    Mass (Da):26,350
    Last modified:August 1, 1988 - v1
    Checksum:i556877A222F0F501
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    J02768 Genomic DNA. Translation: AAA24483.1.
    U00096 Genomic DNA. Translation: AAC74363.1.
    AP009048 Genomic DNA. Translation: BAA14835.1.
    M23250 Genomic DNA. No translation available.
    PIRiA28440. DCECOP.
    RefSeqiNP_415797.1. NC_000913.3.
    YP_489549.1. NC_007779.1.

    Genome annotation databases

    EnsemblBacteriaiAAC74363; AAC74363; b1281.
    BAA14835; BAA14835; BAA14835.
    GeneIDi12931138.
    947121.
    KEGGiecj:Y75_p1256.
    eco:b1281.
    PATRICi32117826. VBIEscCol129921_1333.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    J02768 Genomic DNA. Translation: AAA24483.1 .
    U00096 Genomic DNA. Translation: AAC74363.1 .
    AP009048 Genomic DNA. Translation: BAA14835.1 .
    M23250 Genomic DNA. No translation available.
    PIRi A28440. DCECOP.
    RefSeqi NP_415797.1. NC_000913.3.
    YP_489549.1. NC_007779.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1EIX X-ray 2.50 A/B/C/D 1-245 [» ]
    1JJK X-ray 3.00 A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P 1-245 [» ]
    1L2U X-ray 2.50 A/B 1-245 [» ]
    ProteinModelPortali P08244.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    IntActi P08244. 4 interactions.
    STRINGi 511145.b1281.

    2D gel databases

    SWISS-2DPAGE P08244.

    Proteomic databases

    PaxDbi P08244.
    PRIDEi P08244.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAC74363 ; AAC74363 ; b1281 .
    BAA14835 ; BAA14835 ; BAA14835 .
    GeneIDi 12931138.
    947121.
    KEGGi ecj:Y75_p1256.
    eco:b1281.
    PATRICi 32117826. VBIEscCol129921_1333.

    Organism-specific databases

    EchoBASEi EB0802.
    EcoGenei EG10809. pyrF.

    Phylogenomic databases

    eggNOGi COG0284.
    HOGENOMi HOG000226071.
    KOi K01591.
    OMAi RPITQSA.
    OrthoDBi EOG6N6815.
    PhylomeDBi P08244.

    Enzyme and pathway databases

    UniPathwayi UPA00070 ; UER00120 .
    BioCyci EcoCyc:OROTPDECARB-MONOMER.
    ECOL316407:JW1273-MONOMER.
    MetaCyc:OROTPDECARB-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei P08244.
    PROi P08244.

    Gene expression databases

    Genevestigatori P08244.

    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. "Nucleotide sequence and characterization of the pyrF operon of Escherichia coli K12."
      Turnbough C.L. Jr., Kerr K.H., Funderburg W.R., Donahue J.P., Powell F.E.
      J. Biol. Chem. 262:10239-10245(1987) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: K12.
    2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    4. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
      Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
      Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    5. "A consensus sequence of three DNA replication terminus sites on the E. coli chromosome is highly homologous to the terR sites of the R6K plasmid."
      Hidaka M., Akiyama M., Horiuchi T.
      Cell 55:467-475(1988) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-14.
    6. "Structural basis for the catalytic mechanism of a proficient enzyme: orotidine 5'-monophosphate decarboxylase."
      Harris P., Poulsen J.-C.N., Jensen K.F., Larsen S.
      Biochemistry 39:4217-4224(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOG, SUBUNIT.
      Strain: K12 / MC4100 / ATCC 35695 / DSM 6574.
    7. "Selenomethionine substitution of orotidine-5'-monophosphate decarboxylase causes a change in crystal contacts and space group."
      Poulsen J.-C.N., Harris P., Jensen K.F., Larsen S.
      Acta Crystallogr. D 57:1251-1259(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOG, SUBUNIT.
      Strain: K12 / MC4100 / ATCC 35695 / DSM 6574.
    8. "Substrate binding induces domain movements in orotidine 5'-monophosphate decarboxylase."
      Harris P., Poulsen J.-C.N., Jensen K.F., Larsen S.
      J. Mol. Biol. 318:1019-1029(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF THE NATIVE PROTEIN, SUBUNIT.
      Strain: K12 / MC4100 / ATCC 35695 / DSM 6574.

    Entry informationi

    Entry nameiPYRF_ECOLI
    AccessioniPrimary (citable) accession number: P08244
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: August 1, 1988
    Last sequence update: August 1, 1988
    Last modified: October 1, 2014
    This is version 131 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. Escherichia coli
      Escherichia coli (strain K12): entries and cross-references to EcoGene
    2. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    3. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    4. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3