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Protein

Dihydroorotate dehydrogenase B (NAD(+)), electron transfer subunit

Gene

pyrK

Organism
Lactococcus lactis subsp. cremoris (strain MG1363)
Status
Reviewed-Annotation score:

Annotation score:4 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

Responsible for channeling the electrons from the oxidation of dihydroorotate from the FMN redox center in the PyrDB subunit to the ultimate electron acceptor NAD+.1 Publication

<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

Protein has several cofactor binding sites:

<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 indicates at which position the protein binds a given metal ion. The nature of the metal is indicated in the ‘Description’ field.<p><a href='/help/metal' target='_top'>More...</a></p>Metal bindingi226Iron-sulfur (2Fe-2S)1
Metal bindingi231Iron-sulfur (2Fe-2S)1
Metal bindingi234Iron-sulfur (2Fe-2S)1
Metal bindingi249Iron-sulfur (2Fe-2S)1

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 bindingi53 – 56FAD4
Nucleotide bindingi70 – 72FAD3
Nucleotide bindingi79 – 80FAD2

<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

Biological processElectron transport, Pyrimidine biosynthesis, Transport
Ligand2Fe-2S, FAD, Flavoprotein, Iron, Iron-sulfur, Metal-binding

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...
BioCyci
LLAC416870:LLMG_RS05610-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(+)), electron transfer subunit
Alternative name(s):
Dihydroorotate oxidase B, electron transfer subunit
<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:pyrK
Ordered Locus Names:llmg_1105
<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_00001483631 – 262Dihydroorotate dehydrogenase B (NAD(+)), electron transfer subunitAdd BLAST262

Proteomic databases

PRoteomics IDEntifications database

More...
PRIDEi
P56968

<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
pyrDBP543223EBI-1030589,EBI-1030598

Protein-protein interaction databases

Protein interaction database and analysis system

More...
IntActi
P56968, 1 interactor

Molecular INTeraction database

More...
MINTi
P56968

STRING: functional protein association networks

More...
STRINGi
416870.llmg_1105

<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

1262
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
P56968

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

More...
SMRi
P56968

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
P56968

<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

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/family_and_domains_section">Family and Domains</a> section describes the position and type of a domain, which is defined as a specific combination of secondary structures organized into a characteristic three-dimensional structure or fold.<p><a href='/help/domain' target='_top'>More...</a></p>Domaini3 – 104FAD-binding FR-typeAdd BLAST102

<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

Belongs to the PyrK family.Curated

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
ENOG4105DF0 Bacteria
COG0543 LUCA

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
HOG000225118

KEGG Orthology (KO)

More...
KOi
K02823

Identification of Orthologs from Complete Genome Data

More...
OMAi
RYMKCGI

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

More...
Gene3Di
2.10.240.10, 1 hit
3.40.50.80, 1 hit

HAMAP database of protein families

More...
HAMAPi
MF_01211 DHODB_Fe_S_bind, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR012165 Cyt_c3_hydrogenase_gsu
IPR037117 Dihydroorotate_DH_ele_sf
IPR019480 Dihydroorotate_DH_Fe-S-bd
IPR023455 Dihydroorotate_DHASE_ETsu
IPR017927 FAD-bd_FR_type
IPR039261 FNR_nucleotide-bd
IPR001433 OxRdtase_FAD/NAD-bd
IPR000951 Ph_dOase_redase
IPR017938 Riboflavin_synthase-like_b-brl

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF10418 DHODB_Fe-S_bind, 1 hit
PF00175 NAD_binding_1, 1 hit

PIRSF; a whole-protein classification database

More...
PIRSFi
PIRSF006816 Cyc3_hyd_g, 1 hit

Protein Motif fingerprint database; a protein domain database

More...
PRINTSi
PR00409 PHDIOXRDTASE

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF52343 SSF52343, 1 hit
SSF63380 SSF63380, 1 hit

PROSITE; a protein domain and family database

More...
PROSITEi
View protein in PROSITE
PS51384 FAD_FR, 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.

P56968-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MSQLQEMMTV VSQREVAYNI FEMVLKGTLV DEMDLPGQFL HLAVPNGAML
60 70 80 90 100
LRRPISISSW DKRAKTCTIL YRIGDETTGT YKLSKLESGA KVDVMGPLGN
110 120 130 140 150
GFPVAEVTST DKILIIGGGI GVPPLYELAK QLEKTGCQMT ILLGFASENV
160 170 180 190 200
KILENEFSNL KNVTLKIATD DGSYGTKGHV GMLMNEIDFE VDALYTCGAP
210 220 230 240 250
AMLKAVAKKY DQLERLYISM ESRMACGIGA CYACVEHDKE DESHALKVCE
260
DGPVFLGKQL SL
Length:262
Mass (Da):28,660
Last modified:December 1, 2000 - v1
<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:i9373DB3A75200DB3
GO

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 No translation available.
AM406671 Genomic DNA Translation: CAL97699.1

NCBI Reference Sequences

More...
RefSeqi
WP_011835013.1, NC_009004.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...
EnsemblBacteriai
CAL97699; CAL97699; llmg_1105

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
llm:llmg_1105

<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 No translation available.
AM406671 Genomic DNA Translation: CAL97699.1
RefSeqiWP_011835013.1, 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-ray2.20B2-262[»]
1EP2X-ray2.40B2-262[»]
1EP3X-ray2.10B1-262[»]
ProteinModelPortaliP56968
SMRiP56968
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiP56968, 1 interactor
MINTiP56968
STRINGi416870.llmg_1105

Proteomic databases

PRIDEiP56968

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAL97699; CAL97699; llmg_1105
KEGGillm:llmg_1105

Phylogenomic databases

eggNOGiENOG4105DF0 Bacteria
COG0543 LUCA
HOGENOMiHOG000225118
KOiK02823
OMAiRYMKCGI

Enzyme and pathway databases

UniPathwayi
UPA00070;UER00945

BioCyciLLAC416870:LLMG_RS05610-MONOMER

Miscellaneous databases

EvolutionaryTraceiP56968

Family and domain databases

Gene3Di2.10.240.10, 1 hit
3.40.50.80, 1 hit
HAMAPiMF_01211 DHODB_Fe_S_bind, 1 hit
InterProiView protein in InterPro
IPR012165 Cyt_c3_hydrogenase_gsu
IPR037117 Dihydroorotate_DH_ele_sf
IPR019480 Dihydroorotate_DH_Fe-S-bd
IPR023455 Dihydroorotate_DHASE_ETsu
IPR017927 FAD-bd_FR_type
IPR039261 FNR_nucleotide-bd
IPR001433 OxRdtase_FAD/NAD-bd
IPR000951 Ph_dOase_redase
IPR017938 Riboflavin_synthase-like_b-brl
PfamiView protein in Pfam
PF10418 DHODB_Fe-S_bind, 1 hit
PF00175 NAD_binding_1, 1 hit
PIRSFiPIRSF006816 Cyc3_hyd_g, 1 hit
PRINTSiPR00409 PHDIOXRDTASE
SUPFAMiSSF52343 SSF52343, 1 hit
SSF63380 SSF63380, 1 hit
PROSITEiView protein in PROSITE
PS51384 FAD_FR, 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 nameiPYRK_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: P56968
Secondary accession number(s): A2RK89
<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: December 1, 2000
Last sequence update: December 1, 2000
Last modified: December 5, 2018
This is version 122 of the entry and version 1 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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