Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
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)DescriptionActionsGraphical viewLength
    Binding sitei24FMN1
    Binding sitei48Substrate1
    Binding sitei104FMN1
    Binding sitei132FMN1
    Binding sitei132Substrate1
    Active sitei135Nucleophile1
    Binding sitei170FMN1
    Binding sitei196FMN; via carbonyl oxygen1
    Binding sitei222FMN; via amide nitrogen1

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Nucleotide bindingi48 – 49FMN2
    Nucleotide bindingi248 – 249FMN2
    Nucleotide bindingi270 – 271FMN2

    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

    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)DescriptionActionsGraphical viewLength
    ChainiPRO_00001483961 – 311Dihydroorotate dehydrogenase B (NAD(+)), catalytic subunitAdd BLAST311

    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 interactor.
    MINTiMINT-159259.
    STRINGi416870.llmg_1106.

    Structurei

    Secondary structure

    1311
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Turni5 – 7Combined sources3
    Beta strandi9 – 11Combined sources3
    Beta strandi14 – 22Combined sources9
    Helixi33 – 35Combined sources3
    Helixi39 – 41Combined sources3
    Beta strandi45 – 50Combined sources6
    Beta strandi63 – 66Combined sources4
    Beta strandi69 – 72Combined sources4
    Helixi81 – 86Combined sources6
    Helixi88 – 95Combined sources8
    Beta strandi101 – 105Combined sources5
    Helixi110 – 120Combined sources11
    Beta strandi126 – 132Combined sources7
    Beta strandi135 – 137Combined sources3
    Helixi138 – 140Combined sources3
    Helixi145 – 147Combined sources3
    Helixi149 – 162Combined sources14
    Beta strandi167 – 171Combined sources5
    Helixi179 – 187Combined sources9
    Beta strandi191 – 195Combined sources5
    Beta strandi199 – 201Combined sources3
    Turni206 – 208Combined sources3
    Beta strandi210 – 213Combined sources4
    Beta strandi218 – 222Combined sources5
    Helixi223 – 225Combined sources3
    Helixi226 – 237Combined sources12
    Beta strandi244 – 246Combined sources3
    Helixi253 – 262Combined sources10
    Beta strandi265 – 269Combined sources5
    Helixi272 – 275Combined sources4
    Helixi279 – 293Combined sources15
    Helixi299 – 308Combined sources10

    3D structure databases

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

    Miscellaneous databases

    EvolutionaryTraceiP54322.

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni72 – 76Substrate binding5
    Regioni197 – 198Substrate binding2

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiENOG4107RY0. Bacteria.
    COG0167. LUCA.
    HOGENOMiHOG000225105.
    KOiK17828.
    OMAiKEPRFGN.

    Family and domain databases

    CDDicd04740. DHOD_1B_like. 1 hit.
    Gene3Di3.20.20.70. 1 hit.
    HAMAPiMF_00224. DHO_dh_type1. 1 hit.
    InterProiIPR013785. Aldolase_TIM.
    IPR033888. DHOD_1B.
    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)DescriptionActionsGraphical viewLength
    Sequence conflicti123A → R in CAA52280 (PubMed:8021180).Curated1
    Sequence conflicti123A → R (PubMed:8759867).Curated1
    Sequence conflicti239V → D in CAA52280 (PubMed:8021180).Curated1
    Sequence conflicti239V → D (PubMed:8759867).Curated1
    Sequence conflicti255D → V in CAA52280 (PubMed:8021180).Curated1
    Sequence conflicti255D → V (PubMed:8759867).Curated1
    Sequence conflicti266A → R in CAA52280 (PubMed:8021180).Curated1
    Sequence conflicti266A → R (PubMed:8759867).Curated1

    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
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1EP1X-ray2.20A1-311[»]
    1EP2X-ray2.40A1-311[»]
    1EP3X-ray2.10A1-311[»]
    ProteinModelPortaliP54322.
    SMRiP54322.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    IntActiP54322. 1 interactor.
    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.
    OMAiKEPRFGN.

    Enzyme and pathway databases

    UniPathwayiUPA00070; UER00945.

    Miscellaneous databases

    EvolutionaryTraceiP54322.

    Family and domain databases

    CDDicd04740. DHOD_1B_like. 1 hit.
    Gene3Di3.20.20.70. 1 hit.
    HAMAPiMF_00224. DHO_dh_type1. 1 hit.
    InterProiIPR013785. Aldolase_TIM.
    IPR033888. DHOD_1B.
    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...

    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: November 30, 2016
    This is version 122 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.