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Protein

Probable dihydroorotate dehydrogenase B (NAD(+)), electron transfer subunit

Gene

pyrK

Organism
Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (Pyrococcus kodakaraensis (strain KOD1))
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

Functioni

Responsible for channeling the electrons from the oxidation of dihydroorotate from the FMN redox center in the PyrD type B subunit to the ultimate electron acceptor NAD+.UniRule annotation

Cofactori

Protein has several cofactor binding sites:
  • [2Fe-2S] clusterUniRule annotationNote: Binds 1 [2Fe-2S] cluster per subunit.UniRule annotation
  • FADUniRule annotationNote: Binds 1 FAD per subunit.UniRule annotation

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).UniRule annotation
Proteins known to be involved in this subpathway in this organism are:
  1. Dihydroorotate dehydrogenase B (NAD(+)), catalytic subunit (pyrD), Probable 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
Metal bindingi202 – 2021Iron-sulfur (2Fe-2S)UniRule annotation
Metal bindingi207 – 2071Iron-sulfur (2Fe-2S)UniRule annotation
Metal bindingi210 – 2101Iron-sulfur (2Fe-2S)UniRule annotation
Metal bindingi218 – 2181Iron-sulfur (2Fe-2S)UniRule annotation

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Biological processi

Electron transport, Pyrimidine biosynthesis, Transport

Keywords - Ligandi

2Fe-2S, FAD, Flavoprotein, Iron, Iron-sulfur, Metal-binding

Enzyme and pathway databases

BioCyciTKOD69014:GH72-1843-MONOMER.
UniPathwayiUPA00070; UER00945.

Names & Taxonomyi

Protein namesi
Recommended name:
Probable dihydroorotate dehydrogenase B (NAD(+)), electron transfer subunitUniRule annotation
Alternative name(s):
Dihydroorotate oxidase B, electron transfer subunitUniRule annotation
Gene namesi
Name:pyrKUniRule annotation
Ordered Locus Names:TK1806
OrganismiThermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (Pyrococcus kodakaraensis (strain KOD1))
Taxonomic identifieri69014 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaThermococciThermococcalesThermococcaceaeThermococcus
Proteomesi
  • UP000000536 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 233233Probable dihydroorotate dehydrogenase B (NAD(+)), electron transfer subunitPRO_0000148382Add
BLAST

Interactioni

Subunit structurei

Heterotetramer of 2 PyrK and 2 PyrD type B subunits.UniRule annotation

Protein-protein interaction databases

STRINGi69014.TK1806.

Structurei

3D structure databases

ProteinModelPortaliQ5JJ90.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini1 – 8787FAD-binding FR-typeUniRule annotationAdd
BLAST

Sequence similaritiesi

Belongs to the PyrK family.UniRule annotation
Contains 1 FAD-binding FR-type domain.UniRule annotation

Phylogenomic databases

eggNOGiarCOG02199. Archaea.
COG0543. LUCA.
HOGENOMiHOG000225118.
InParanoidiQ5JJ90.
KOiK02823.
OMAiMKCGIGV.

Family and domain databases

Gene3Di2.10.240.10. 1 hit.
HAMAPiMF_01211. DHODB_Fe_S_bind. 1 hit.
InterProiIPR012165. Cyt_c3_hydrogenase_gsu.
IPR019480. Dihydroorotate_DH_Fe-S-bd.
IPR023455. Dihydroorotate_DHASE_ETsu.
IPR017927. Fd_Rdtase_FAD-bd.
IPR001433. OxRdtase_FAD/NAD-bd.
IPR000951. Ph_dOase_redase.
IPR017938. Riboflavin_synthase-like_b-brl.
[Graphical view]
PfamiPF10418. DHODB_Fe-S_bind. 1 hit.
PF00175. NAD_binding_1. 1 hit.
[Graphical view]
PIRSFiPIRSF006816. Cyc3_hyd_g. 1 hit.
PRINTSiPR00409. PHDIOXRDTASE.
SUPFAMiSSF63380. SSF63380. 1 hit.
PROSITEiPS00197. 2FE2S_FER_1. 1 hit.
PS51384. FAD_FR. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q5JJ90-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MYRVVTIEEV WDVAKDVKAF RFNENIEFAP GQFIMAWLPG VGEKPFSLAW
60 70 80 90 100
EDMIVVKRVG PFTTKLFELK EGDRLWIRGP YGHGFIKRGE KVALVGGGIG
110 120 130 140 150
IPPLYAFAKK NQGKFRQMTL IYGARSKDEL SLLDIENYVD DAVITTDDGS
160 170 180 190 200
AGRKGFPTEV LAERREEFDQ VYACGPEPML KAVLKVMNYK NVQISAERYM
210 220 230
KCGIGVCGSC NLGKYLVCRD GPVFEGEKLV GLL
Length:233
Mass (Da):26,105
Last modified:February 15, 2005 - v1
Checksum:i8EAF86C10F922704
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP006878 Genomic DNA. Translation: BAD85995.1.
RefSeqiWP_011250757.1. NC_006624.1.

Genome annotation databases

EnsemblBacteriaiBAD85995; BAD85995; TK1806.
GeneIDi3235015.
KEGGitko:TK1806.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP006878 Genomic DNA. Translation: BAD85995.1.
RefSeqiWP_011250757.1. NC_006624.1.

3D structure databases

ProteinModelPortaliQ5JJ90.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi69014.TK1806.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAD85995; BAD85995; TK1806.
GeneIDi3235015.
KEGGitko:TK1806.

Phylogenomic databases

eggNOGiarCOG02199. Archaea.
COG0543. LUCA.
HOGENOMiHOG000225118.
InParanoidiQ5JJ90.
KOiK02823.
OMAiMKCGIGV.

Enzyme and pathway databases

UniPathwayiUPA00070; UER00945.
BioCyciTKOD69014:GH72-1843-MONOMER.

Family and domain databases

Gene3Di2.10.240.10. 1 hit.
HAMAPiMF_01211. DHODB_Fe_S_bind. 1 hit.
InterProiIPR012165. Cyt_c3_hydrogenase_gsu.
IPR019480. Dihydroorotate_DH_Fe-S-bd.
IPR023455. Dihydroorotate_DHASE_ETsu.
IPR017927. Fd_Rdtase_FAD-bd.
IPR001433. OxRdtase_FAD/NAD-bd.
IPR000951. Ph_dOase_redase.
IPR017938. Riboflavin_synthase-like_b-brl.
[Graphical view]
PfamiPF10418. DHODB_Fe-S_bind. 1 hit.
PF00175. NAD_binding_1. 1 hit.
[Graphical view]
PIRSFiPIRSF006816. Cyc3_hyd_g. 1 hit.
PRINTSiPR00409. PHDIOXRDTASE.
SUPFAMiSSF63380. SSF63380. 1 hit.
PROSITEiPS00197. 2FE2S_FER_1. 1 hit.
PS51384. FAD_FR. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiPYRK_THEKO
AccessioniPrimary (citable) accession number: Q5JJ90
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 30, 2005
Last sequence update: February 15, 2005
Last modified: November 11, 2015
This is version 82 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

Complete proteome, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. 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.