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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

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the ‘correct annotation’ for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the ‘protein existence’ evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>Functioni

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

<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section describes the catalytic activity of an enzyme, i.e. a chemical reaction that the enzyme catalyzes.<p><a href='/help/catalytic_activity' target='_top'>More...</a></p>Catalytic activityi

<p>This subsection of the ‘Function’ section provides information relevant to cofactors. A cofactor is any non-protein substance required for a protein to be catalytically active. Some cofactors are inorganic, such as the metal atoms zinc, iron, and copper in various oxidation states. Others, such as most vitamins, are organic.<p><a href='/help/cofactor' target='_top'>More...</a></p>Cofactori

FMN2 PublicationsNote: Binds 1 FMN per subunit.2 Publications

<p>This subsection of the ‘Function’ section describes biophysical and chemical properties, such as maximal absorption, kinetic parameters, pH dependence, redox potentials and temperature dependence.<p><a href='/help/biophysicochemical_properties' target='_top'>More...</a></p>Kineticsi

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

    pH dependencei

    Optimum pH is 8.1 Publication

    <p>This subsection of the <a href="http://www.uniprot.org/help/function_section">'Function'</a> section describes the metabolic pathway(s) associated with a protein.<p><a href='/help/pathway' target='_top'>More...</a></p>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
    <p>This subsection of the ‘Function’ section describes the interaction between a single amino acid and another chemical entity. Priority is given to the annotation of physiological ligands.<p><a href='/help/binding' target='_top'>More...</a></p>Binding sitei24FMN1
    Binding sitei48Substrate1
    Binding sitei104FMN1
    Binding sitei132FMN1
    Binding sitei132Substrate1
    <p>This subsection of the ‘Function’ section is used for enzymes and indicates the residues directly involved in catalysis.<p><a href='/help/act_site' target='_top'>More...</a></p>Active sitei135Nucleophile1
    Binding sitei170FMN1
    Binding sitei196FMN; via carbonyl oxygen1
    Binding sitei222FMN; via amide nitrogen1

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the ‘Function’ section describes a region in the protein which binds nucleotide phosphates. It always involves more than one amino acid and includes all residues involved in nucleotide-binding.<p><a href='/help/np_bind' target='_top'>More...</a></p>Nucleotide bindingi48 – 49FMN2
    Nucleotide bindingi248 – 249FMN2
    Nucleotide bindingi270 – 271FMN2

    <p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

    GO - Biological processi

    <p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

    Molecular functionOxidoreductase
    Biological processPyrimidine biosynthesis
    LigandFlavoprotein, FMN, NAD

    Enzyme and pathway databases

    BioCyc Collection of Pathway/Genome Databases

    More...
    BioCyci
    LLAC416870:LLMG_RS05615-MONOMER

    UniPathway: a resource for the exploration and annotation of metabolic pathways

    More...
    UniPathwayi
    UPA00070;UER00945

    <p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

    <p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>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)
    <p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: ‘Name’, ‘Synonyms’, ‘Ordered locus names’ and ‘ORF names’.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
    Name:pyrDB
    Ordered Locus Names:llmg_1106
    <p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiLactococcus lactis subsp. cremoris (strain MG1363)
    <p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the ‘taxonomic identifier’ or ‘taxid’.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri416870 [NCBI]
    <p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiBacteriaFirmicutesBacilliLactobacillalesStreptococcaceaeLactococcus
    <p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
    • UP000000364 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes_manual">proteome</a> can consist of several components. <br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Chromosome

    <p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

    GO - Cellular componenti

    Keywords - Cellular componenti

    Cytoplasm

    <p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the ‘PTM / Processing’ section describes the extent of a polypeptide chain in the mature protein following processing.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00001483961 – 311Dihydroorotate dehydrogenase B (NAD(+)), catalytic subunitAdd BLAST311

    <p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

    <p>This subsection of the <a href="http://www.uniprot.org/help/interaction_section">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function_section">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

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

    <p>This subsection of the '<a href="http://www.uniprot.org/help/interaction_section%27">Interaction</a> section provides information about binary protein-protein interactions. The data presented in this section are a quality-filtered subset of binary interactions automatically derived from the <a href="http://www.ebi.ac.uk/intact/">IntAct database</a>. It is updated on a monthly basis. Each binary interaction is displayed on a separate line.<p><a href='/help/binary_interactions' target='_top'>More...</a></p>Binary interactionsi

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

    Protein-protein interaction databases

    Protein interaction database and analysis system

    More...
    IntActi
    P54322, 1 interactor

    Molecular INTeraction database

    More...
    MINTi
    P54322

    STRING: functional protein association networks

    More...
    STRINGi
    416870.llmg_1106

    <p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

    Secondary structure

    1311
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details

    3D structure databases

    Protein Model Portal of the PSI-Nature Structural Biology Knowledgebase

    More...
    ProteinModelPortali
    P54322

    SWISS-MODEL Repository - a database of annotated 3D protein structure models

    More...
    SMRi
    P54322

    Database of comparative protein structure models

    More...
    ModBasei
    Search...

    MobiDB: a database of protein disorder and mobility annotations

    More...
    MobiDBi
    Search...

    Miscellaneous databases

    Relative evolutionary importance of amino acids within a protein sequence

    More...
    EvolutionaryTracei
    P54322

    <p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the ‘Family and Domains’ section describes a region of interest that cannot be described in other subsections.<p><a href='/help/region' target='_top'>More...</a></p>Regioni72 – 76Substrate binding5
    Regioni197 – 198Substrate binding2

    <p>This subsection of the ‘Family and domains’ section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

    Phylogenomic databases

    evolutionary genealogy of genes: Non-supervised Orthologous Groups

    More...
    eggNOGi
    ENOG4107RY0 Bacteria
    COG0167 LUCA

    The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

    More...
    HOGENOMi
    HOG000225105

    KEGG Orthology (KO)

    More...
    KOi
    K17828

    Identification of Orthologs from Complete Genome Data

    More...
    OMAi
    SCPHAKG

    Family and domain databases

    Conserved Domains Database

    More...
    CDDi
    cd04740 DHOD_1B_like, 1 hit

    Gene3D Structural and Functional Annotation of Protein Families

    More...
    Gene3Di
    3.20.20.70, 1 hit

    HAMAP database of protein families

    More...
    HAMAPi
    MF_00224 DHO_dh_type1, 1 hit

    Integrated resource of protein families, domains and functional sites

    More...
    InterProi
    View protein in InterPro
    IPR013785 Aldolase_TIM
    IPR033888 DHOD_1B
    IPR005720 Dihydroorotate_DH
    IPR024920 Dihydroorotate_DH_1
    IPR012135 Dihydroorotate_DH_1_2
    IPR001295 Dihydroorotate_DH_CS

    Pfam protein domain database

    More...
    Pfami
    View protein in Pfam
    PF01180 DHO_dh, 1 hit

    PIRSF; a whole-protein classification database

    More...
    PIRSFi
    PIRSF000164 DHO_oxidase, 1 hit

    TIGRFAMs; a protein family database

    More...
    TIGRFAMsi
    TIGR01037 pyrD_sub1_fam, 1 hit

    PROSITE; a protein domain and family database

    More...
    PROSITEi
    View protein in PROSITE
    PS00911 DHODEHASE_1, 1 hit
    PS00912 DHODEHASE_2, 1 hit

    <p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence_length">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>.<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

    <p>This subsection of the <a href="http://www.uniprot.org/help/sequences_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>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
    <p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:i1854517E5B585BB9
    GO

    Experimental Info

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the ‘Sequence’ section reports difference(s) between the canonical sequence (displayed by default in the entry) and the different sequence submissions merged in the entry. These various submissions may originate from different sequencing projects, different types of experiments, or different biological samples. Sequence conflicts are usually of unknown origin.<p><a href='/help/conflict' target='_top'>More...</a></p>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:

    EMBL nucleotide sequence database

    More...
    EMBLi

    GenBank nucleotide sequence database

    More...
    GenBanki

    DNA Data Bank of Japan; a nucleotide sequence database

    More...
    DDBJi
    Links Updated
    X74207 Genomic DNA Translation: CAA52280.1
    AM406671 Genomic DNA Translation: CAL97700.1

    NCBI Reference Sequences

    More...
    RefSeqi
    WP_011835014.1, NC_009004.1

    Genome annotation databases

    Ensembl bacterial and archaeal genome annotation project

    More...
    EnsemblBacteriai
    CAL97700; CAL97700; llmg_1106

    KEGG: Kyoto Encyclopedia of Genes and Genomes

    More...
    KEGGi
    llm:llmg_1106

    <p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

    <p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>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:

    Protein Data Bank Europe

    More...
    PDBei

    Protein Data Bank RCSB

    More...
    RCSB PDBi

    Protein Data Bank Japan

    More...
    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
    MINTiP54322
    STRINGi416870.llmg_1106

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiCAL97700; CAL97700; llmg_1106
    KEGGillm:llmg_1106

    Phylogenomic databases

    eggNOGiENOG4107RY0 Bacteria
    COG0167 LUCA
    HOGENOMiHOG000225105
    KOiK17828
    OMAiSCPHAKG

    Enzyme and pathway databases

    UniPathwayi
    UPA00070;UER00945

    BioCyciLLAC416870:LLMG_RS05615-MONOMER

    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
    InterProiView protein in InterPro
    IPR013785 Aldolase_TIM
    IPR033888 DHOD_1B
    IPR005720 Dihydroorotate_DH
    IPR024920 Dihydroorotate_DH_1
    IPR012135 Dihydroorotate_DH_1_2
    IPR001295 Dihydroorotate_DH_CS
    PfamiView protein in Pfam
    PF01180 DHO_dh, 1 hit
    PIRSFiPIRSF000164 DHO_oxidase, 1 hit
    TIGRFAMsiTIGR01037 pyrD_sub1_fam, 1 hit
    PROSITEiView protein in PROSITE
    PS00911 DHODEHASE_1, 1 hit
    PS00912 DHODEHASE_2, 1 hit

    ProtoNet; Automatic hierarchical classification of proteins

    More...
    ProtoNeti
    Search...

    <p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

    <p>This subsection of the ‘Entry information’ section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiPYRDB_LACLM
    <p>This subsection of the ‘Entry information’ section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called ‘Primary (citable) accession number’.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: P54322
    Secondary accession number(s): A2RK90
    <p>This subsection of the ‘Entry information’ section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification (‘Last modified’). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: October 1, 1996
    Last sequence update: May 1, 2007
    Last modified: December 5, 2018
    This is version 128 of the entry and version 2 of the sequence. See complete history.
    <p>This subsection of the ‘Entry information’ section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    <p>This section contains any relevant information that doesn’t fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. SIMILARITY comments
      Index of protein domains and families
    3. PATHWAY comments
      Index of metabolic and biosynthesis pathways
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