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Protein

Dihydroorotate dehydrogenase B (NAD(+)), catalytic subunit

Gene

pyrDB

Organism
Lactococcus lactis subsp. cremoris (strain MG1363)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the conversion of dihydroorotate to orotate with NAD+ as electron acceptor. Cannot use fumarate as an electron acceptor.1 Publication

Catalytic activityi

(S)-dihydroorotate + NAD+ = orotate + NADH.2 Publications

Cofactori

FMN2 PublicationsNote: Binds 1 FMN per subunit.2 Publications

Kineticsi

  1. KM=28 µM for orotate1 Publication
  2. KM=111 µM for NAD+1 Publication

    pH dependencei

    Optimum pH is 8.1 Publication

    Pathwayi: UMP biosynthesis via de novo pathway

    This protein is involved in step 1 of the subpathway that synthesizes orotate from (S)-dihydroorotate (NAD(+) route).
    Proteins known to be involved in this subpathway in this organism are:
    1. Dihydroorotate dehydrogenase B (NAD(+)), catalytic subunit (pyrDB), Dihydroorotate dehydrogenase B (NAD(+)), electron transfer subunit (pyrK)
    This subpathway is part of the pathway UMP biosynthesis via de novo pathway, which is itself part of Pyrimidine metabolism.
    View all proteins of this organism that are known to be involved in the subpathway that synthesizes orotate from (S)-dihydroorotate (NAD(+) route), the pathway UMP biosynthesis via de novo pathway and in Pyrimidine metabolism.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei24 – 241FMN
    Binding sitei48 – 481Substrate
    Binding sitei104 – 1041FMN
    Binding sitei132 – 1321FMN
    Binding sitei132 – 1321Substrate
    Active sitei135 – 1351Nucleophile
    Binding sitei170 – 1701FMN
    Binding sitei196 – 1961FMN; via carbonyl oxygen
    Binding sitei222 – 2221FMN; via amide nitrogen

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi48 – 492FMN
    Nucleotide bindingi248 – 2492FMN
    Nucleotide bindingi270 – 2712FMN

    GO - Molecular functioni

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Biological processi

    Pyrimidine biosynthesis

    Keywords - Ligandi

    Flavoprotein, FMN, NAD

    Enzyme and pathway databases

    BioCyciLLAC416870:GCDT-1132-MONOMER.
    UniPathwayiUPA00070; UER00945.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Dihydroorotate dehydrogenase B (NAD(+)), catalytic subunit (EC:1.3.1.14)
    Short name:
    DHOD B
    Short name:
    DHODase B
    Short name:
    DHOdehase B
    Alternative name(s):
    Dihydroorotate oxidase B
    Orotate reductase (NADH)
    Gene namesi
    Name:pyrDB
    Ordered Locus Names:llmg_1106
    OrganismiLactococcus lactis subsp. cremoris (strain MG1363)
    Taxonomic identifieri416870 [NCBI]
    Taxonomic lineageiBacteriaFirmicutesBacilliLactobacillalesStreptococcaceaeLactococcus
    Proteomesi
    • UP000000364 Componenti: Chromosome

    Subcellular locationi

    GO - Cellular componenti

    Complete GO annotation...

    Keywords - Cellular componenti

    Cytoplasm

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 311311Dihydroorotate dehydrogenase B (NAD(+)), catalytic subunitPRO_0000148396Add
    BLAST

    Interactioni

    Subunit structurei

    Heterotetramer of 2 PyrK and 2 PyrD type B subunits.1 Publication

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    pyrKP569683EBI-1030598,EBI-1030589

    Protein-protein interaction databases

    IntActiP54322. 1 interaction.
    MINTiMINT-159259.
    STRINGi416870.llmg_1106.

    Structurei

    Secondary structure

    1
    311
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Turni5 – 73Combined sources
    Beta strandi9 – 113Combined sources
    Beta strandi14 – 229Combined sources
    Helixi33 – 353Combined sources
    Helixi39 – 413Combined sources
    Beta strandi45 – 506Combined sources
    Beta strandi63 – 664Combined sources
    Beta strandi69 – 724Combined sources
    Helixi81 – 866Combined sources
    Helixi88 – 958Combined sources
    Beta strandi101 – 1055Combined sources
    Helixi110 – 12011Combined sources
    Beta strandi126 – 1327Combined sources
    Beta strandi135 – 1373Combined sources
    Helixi138 – 1403Combined sources
    Helixi145 – 1473Combined sources
    Helixi149 – 16214Combined sources
    Beta strandi167 – 1715Combined sources
    Helixi179 – 1879Combined sources
    Beta strandi191 – 1955Combined sources
    Beta strandi199 – 2013Combined sources
    Turni206 – 2083Combined sources
    Beta strandi210 – 2134Combined sources
    Beta strandi218 – 2225Combined sources
    Helixi223 – 2253Combined sources
    Helixi226 – 23712Combined sources
    Beta strandi244 – 2463Combined sources
    Helixi253 – 26210Combined sources
    Beta strandi265 – 2695Combined sources
    Helixi272 – 2754Combined sources
    Helixi279 – 29315Combined sources
    Helixi299 – 30810Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1EP1X-ray2.20A1-311[»]
    1EP2X-ray2.40A1-311[»]
    1EP3X-ray2.10A1-311[»]
    ProteinModelPortaliP54322.
    SMRiP54322. Positions 1-311.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP54322.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni72 – 765Substrate binding
    Regioni197 – 1982Substrate binding

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiENOG4107RY0. Bacteria.
    COG0167. LUCA.
    HOGENOMiHOG000225105.
    KOiK17828.
    OMAiHAVQIGT.
    OrthoDBiEOG6NPM9S.

    Family and domain databases

    Gene3Di3.20.20.70. 1 hit.
    HAMAPiMF_00224. DHO_dh_type1.
    InterProiIPR013785. Aldolase_TIM.
    IPR005720. Dihydroorotate_DH.
    IPR024920. Dihydroorotate_DH_1.
    IPR012135. Dihydroorotate_DH_1_2.
    IPR001295. Dihydroorotate_DH_CS.
    [Graphical view]
    PfamiPF01180. DHO_dh. 1 hit.
    [Graphical view]
    PIRSFiPIRSF000164. DHO_oxidase. 1 hit.
    TIGRFAMsiTIGR01037. pyrD_sub1_fam. 1 hit.
    PROSITEiPS00911. DHODEHASE_1. 1 hit.
    PS00912. DHODEHASE_2. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P54322-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MTENNRLSVK LPGLDLKNPI IPASGCFGFG EEYAKYYDLN KLGSIMVKAT
    60 70 80 90 100
    TLHPRFGNPT PRVAETASGM LNAIGLQNPG LEVIMTEKLP WLNENFPELP
    110 120 130 140 150
    IIANVAGSEE ADYVAVCAKI GDAANVKAIE LNISCPNVKH GGQAFGTDPE
    160 170 180 190 200
    VAAALVKACK AVSKVPLYVK LSPNVTDIVP IAKAVEAAGA DGLTMINTLM
    210 220 230 240 250
    GVRFDLKTRQ PILANITGGL SGPAIKPVAL KLIHQVAQVV DIPIIGMGGV
    260 270 280 290 300
    ANAQDVLEMY MAGASAVAVG TANFADPFVC PKIIDKLPEL MDQYRIESLE
    310
    SLIQEVKEGK K
    Length:311
    Mass (Da):32,930
    Last modified:May 1, 2007 - v2
    Checksum:i1854517E5B585BB9
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti123 – 1231A → R in CAA52280 (PubMed:8021180).Curated
    Sequence conflicti123 – 1231A → R (PubMed:8759867).Curated
    Sequence conflicti239 – 2391V → D in CAA52280 (PubMed:8021180).Curated
    Sequence conflicti239 – 2391V → D (PubMed:8759867).Curated
    Sequence conflicti255 – 2551D → V in CAA52280 (PubMed:8021180).Curated
    Sequence conflicti255 – 2551D → V (PubMed:8759867).Curated
    Sequence conflicti266 – 2661A → R in CAA52280 (PubMed:8021180).Curated
    Sequence conflicti266 – 2661A → R (PubMed:8759867).Curated

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    X74207 Genomic DNA. Translation: CAA52280.1.
    AM406671 Genomic DNA. Translation: CAL97700.1.
    RefSeqiWP_011835014.1. NC_009004.1.

    Genome annotation databases

    EnsemblBacteriaiCAL97700; CAL97700; llmg_1106.
    KEGGillm:llmg_1106.
    PATRICi22283360. VBILacLac4574_1137.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    X74207 Genomic DNA. Translation: CAA52280.1.
    AM406671 Genomic DNA. Translation: CAL97700.1.
    RefSeqiWP_011835014.1. NC_009004.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1EP1X-ray2.20A1-311[»]
    1EP2X-ray2.40A1-311[»]
    1EP3X-ray2.10A1-311[»]
    ProteinModelPortaliP54322.
    SMRiP54322. Positions 1-311.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    IntActiP54322. 1 interaction.
    MINTiMINT-159259.
    STRINGi416870.llmg_1106.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiCAL97700; CAL97700; llmg_1106.
    KEGGillm:llmg_1106.
    PATRICi22283360. VBILacLac4574_1137.

    Phylogenomic databases

    eggNOGiENOG4107RY0. Bacteria.
    COG0167. LUCA.
    HOGENOMiHOG000225105.
    KOiK17828.
    OMAiHAVQIGT.
    OrthoDBiEOG6NPM9S.

    Enzyme and pathway databases

    UniPathwayiUPA00070; UER00945.
    BioCyciLLAC416870:GCDT-1132-MONOMER.

    Miscellaneous databases

    EvolutionaryTraceiP54322.

    Family and domain databases

    Gene3Di3.20.20.70. 1 hit.
    HAMAPiMF_00224. DHO_dh_type1.
    InterProiIPR013785. Aldolase_TIM.
    IPR005720. Dihydroorotate_DH.
    IPR024920. Dihydroorotate_DH_1.
    IPR012135. Dihydroorotate_DH_1_2.
    IPR001295. Dihydroorotate_DH_CS.
    [Graphical view]
    PfamiPF01180. DHO_dh. 1 hit.
    [Graphical view]
    PIRSFiPIRSF000164. DHO_oxidase. 1 hit.
    TIGRFAMsiTIGR01037. pyrD_sub1_fam. 1 hit.
    PROSITEiPS00911. DHODEHASE_1. 1 hit.
    PS00912. DHODEHASE_2. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. "Two different dihydroorotate dehydrogenases in Lactococcus lactis."
      Andersen P.S., Jansen P.J.G., Hammer K.
      J. Bacteriol. 176:3975-3982(1994) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY.
      Strain: MG1363.
    2. "Sequence analysis and identification of the pyrKDbF operon from Lactococcus lactis including a novel gene, pyrK, involved in pyrimidine biosynthesis."
      Andersen P.S., Martinussen J., Hammer K.
      J. Bacteriol. 178:5005-5012(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: MG1363.
    3. "The complete genome sequence of the lactic acid bacterial paradigm Lactococcus lactis subsp. cremoris MG1363."
      Wegmann U., O'Connell-Motherway M., Zomer A., Buist G., Shearman C., Canchaya C., Ventura M., Goesmann A., Gasson M.J., Kuipers O.P., van Sinderen D., Kok J.
      J. Bacteriol. 189:3256-3270(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: MG1363.
    4. "The B form of dihydroorotate dehydrogenase from Lactococcus lactis consists of two different subunits, encoded by the pyrDb and pyrK genes, and contains FMN, FAD, and [FeS] redox centers."
      Nielsen F.S., Andersen P.S., Jensen K.F.
      J. Biol. Chem. 271:29359-29365(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: CATALYTIC ACTIVITY, COFACTOR, SUBUNIT, BIOPHYSICOCHEMICAL PROPERTIES.
      Strain: MG1363.
    5. "Structure of dihydroorotate dehydrogenase B: electron transfer between two flavin groups bridged by an iron-sulphur cluster."
      Rowland P., Noerager S., Jensen K.F., Larsen S.
      Structure 8:1227-1238(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) IN COMPLEXES WITH FMN AND OROTATE, COFACTOR, REACTION MECHANISM.
      Strain: MG1363.

    Entry informationi

    Entry nameiPYRDB_LACLM
    AccessioniPrimary (citable) accession number: P54322
    Secondary accession number(s): A2RK90
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 1, 1996
    Last sequence update: May 1, 2007
    Last modified: June 8, 2016
    This is version 118 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

    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

    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 one 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.