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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-Experimental evidence at protein leveli

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

Cofactori

Protein has several cofactor binding sites:

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

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:
Dihydroorotate dehydrogenase B (NAD(+)), electron transfer subunit
Alternative name(s):
Dihydroorotate oxidase B, electron transfer subunit
Gene namesi
Name:pyrK
Ordered Locus Names:llmg_1105
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_00001483631 – 262Dihydroorotate dehydrogenase B (NAD(+)), electron transfer subunitAdd BLAST262

Interactioni

Subunit structurei

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

Binary interactionsi

WithEntry#Exp.IntActNotes
pyrDBP543223EBI-1030589,EBI-1030598

Protein-protein interaction databases

IntActiP56968. 1 interactor.
MINTiMINT-159270.
STRINGi416870.llmg_1105.

Structurei

Secondary structure

1262
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi4 – 17Combined sources14
Beta strandi20 – 27Combined sources8
Helixi28 – 32Combined sources5
Beta strandi39 – 42Combined sources4
Beta strandi53 – 56Combined sources4
Beta strandi59 – 61Combined sources3
Turni62 – 65Combined sources4
Beta strandi66 – 72Combined sources7
Helixi79 – 84Combined sources6
Beta strandi91 – 100Combined sources10
Beta strandi111 – 118Combined sources8
Helixi119 – 121Combined sources3
Helixi123 – 134Combined sources12
Beta strandi138 – 147Combined sources10
Helixi148 – 150Combined sources3
Helixi154 – 158Combined sources5
Beta strandi163 – 169Combined sources7
Beta strandi173 – 178Combined sources6
Helixi180 – 186Combined sources7
Beta strandi192 – 198Combined sources7
Helixi200 – 209Combined sources10
Turni210 – 212Combined sources3
Beta strandi214 – 219Combined sources6
Beta strandi225 – 231Combined sources7
Beta strandi235 – 238Combined sources4
Beta strandi241 – 247Combined sources7
Turni248 – 251Combined sources4
Beta strandi253 – 256Combined sources4
Turni257 – 260Combined sources4

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1EP1X-ray2.20B2-262[»]
1EP2X-ray2.40B2-262[»]
1EP3X-ray2.10B1-262[»]
ProteinModelPortaliP56968.
SMRiP56968.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP56968.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini3 – 104FAD-binding FR-typeAdd BLAST102

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiENOG4105DF0. Bacteria.
COG0543. LUCA.
HOGENOMiHOG000225118.
KOiK02823.
OMAiEEKMACG.

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.
PROSITEiPS51384. FAD_FR. 1 hit.
[Graphical view]

Sequencei

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
Checksum:i9373DB3A75200DB3
GO

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.

Genome annotation databases

EnsemblBacteriaiCAL97699; CAL97699; llmg_1105.
KEGGillm:llmg_1105.
PATRICi22283358. VBILacLac4574_1136.

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:
PDBei
RCSB PDBi
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.
MINTiMINT-159270.
STRINGi416870.llmg_1105.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAL97699; CAL97699; llmg_1105.
KEGGillm:llmg_1105.
PATRICi22283358. VBILacLac4574_1136.

Phylogenomic databases

eggNOGiENOG4105DF0. Bacteria.
COG0543. LUCA.
HOGENOMiHOG000225118.
KOiK02823.
OMAiEEKMACG.

Enzyme and pathway databases

UniPathwayiUPA00070; UER00945.

Miscellaneous databases

EvolutionaryTraceiP56968.

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.
PROSITEiPS51384. FAD_FR. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiPYRK_LACLM
AccessioniPrimary (citable) accession number: P56968
Secondary accession number(s): A2RK89
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 1, 2000
Last sequence update: December 1, 2000
Last modified: November 2, 2016
This is version 112 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

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.