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Protein

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

Gene

pyrK

Organism
Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (Methanococcus jannaschii)
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 bindingi208 – 2081Iron-sulfur (2Fe-2S)UniRule annotation
Metal bindingi213 – 2131Iron-sulfur (2Fe-2S)UniRule annotation
Metal bindingi216 – 2161Iron-sulfur (2Fe-2S)UniRule annotation
Metal bindingi226 – 2261Iron-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

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:MJ1446
OrganismiMethanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (Methanococcus jannaschii)
Taxonomic identifieri243232 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaMethanococciMethanococcalesMethanocaldococcaceaeMethanocaldococcus
Proteomesi
  • UP000000805 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 257257Probable dihydroorotate dehydrogenase B (NAD(+)), electron transfer subunitPRO_0000148375Add
BLAST

Interactioni

Subunit structurei

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

Protein-protein interaction databases

STRINGi243232.MJ_1446.

Structurei

3D structure databases

ProteinModelPortaliQ58841.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini2 – 8988FAD-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.
InParanoidiQ58841.
KOiK02823.
OMAiMKCGIGV.
PhylomeDBiQ58841.

Family and domain databases

Gene3Di2.10.240.10. 1 hit.
HAMAPiMF_01211. DHODB_Fe_S_bind.
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.
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.
SUPFAMiSSF63380. SSF63380. 1 hit.
PROSITEiPS00197. 2FE2S_FER_1. 1 hit.
PS51384. FAD_FR. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q58841-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MEKPVICRIK EIIEESPTVK TFVVDKDFDF KPGQFAMLWL PGVDEKPFGF
60 70 80 90 100
SSKNSFSVAR VGEFTKKMHE LKEGDIIGVR GPYGTYFEPI GDKVLAVAGG
110 120 130 140 150
IGAAPIITAV EEFSKQGIEI TTILGARTKE ELLFLDRFEK VSRLEICTDD
160 170 180 190 200
GSFGFKGFTT EKMKEVLKEE KFDLIITCGP EIMMKKVVEI ANEYNIPVQV
210 220 230 240 250
SMERYMKCGI GICGQCCVDD EGLCVCKDGP VFWGDKLKFI REFGKYKRDA

SGKKIYY
Length:257
Mass (Da):28,908
Last modified:November 1, 1996 - v1
Checksum:i08D463BFE1CD432D
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L77117 Genomic DNA. Translation: AAB99455.1.
PIRiE64480.

Genome annotation databases

EnsemblBacteriaiAAB99455; AAB99455; MJ_1446.
KEGGimja:MJ_1446.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L77117 Genomic DNA. Translation: AAB99455.1.
PIRiE64480.

3D structure databases

ProteinModelPortaliQ58841.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi243232.MJ_1446.

Protocols and materials databases

DNASUi1452350.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAB99455; AAB99455; MJ_1446.
KEGGimja:MJ_1446.

Phylogenomic databases

eggNOGiarCOG02199. Archaea.
COG0543. LUCA.
InParanoidiQ58841.
KOiK02823.
OMAiMKCGIGV.
PhylomeDBiQ58841.

Enzyme and pathway databases

UniPathwayiUPA00070; UER00945.

Family and domain databases

Gene3Di2.10.240.10. 1 hit.
HAMAPiMF_01211. DHODB_Fe_S_bind.
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.
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.
SUPFAMiSSF63380. SSF63380. 1 hit.
PROSITEiPS00197. 2FE2S_FER_1. 1 hit.
PS51384. FAD_FR. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440.

Entry informationi

Entry nameiPYRK_METJA
AccessioniPrimary (citable) accession number: Q58841
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 1, 2000
Last sequence update: November 1, 1996
Last modified: July 6, 2016
This is version 120 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. Methanococcus jannaschii
    Methanococcus jannaschii: entries and gene names
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  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.