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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)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi226 – 2261Iron-sulfur (2Fe-2S)
Metal bindingi231 – 2311Iron-sulfur (2Fe-2S)
Metal bindingi234 – 2341Iron-sulfur (2Fe-2S)
Metal bindingi249 – 2491Iron-sulfur (2Fe-2S)

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi53 – 564FAD
Nucleotide bindingi70 – 723FAD
Nucleotide bindingi79 – 802FAD

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

BioCyciLLAC416870:GCDT-1131-MONOMER.
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)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 262262Dihydroorotate dehydrogenase B (NAD(+)), electron transfer subunitPRO_0000148363Add
BLAST

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 interaction.
MINTiMINT-159270.
STRINGi416870.llmg_1105.

Structurei

Secondary structure

1
262
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi4 – 1714Combined sources
Beta strandi20 – 278Combined sources
Helixi28 – 325Combined sources
Beta strandi39 – 424Combined sources
Beta strandi53 – 564Combined sources
Beta strandi59 – 613Combined sources
Turni62 – 654Combined sources
Beta strandi66 – 727Combined sources
Helixi79 – 846Combined sources
Beta strandi91 – 10010Combined sources
Beta strandi111 – 1188Combined sources
Helixi119 – 1213Combined sources
Helixi123 – 13412Combined sources
Beta strandi138 – 14710Combined sources
Helixi148 – 1503Combined sources
Helixi154 – 1585Combined sources
Beta strandi163 – 1697Combined sources
Beta strandi173 – 1786Combined sources
Helixi180 – 1867Combined sources
Beta strandi192 – 1987Combined sources
Helixi200 – 20910Combined sources
Turni210 – 2123Combined sources
Beta strandi214 – 2196Combined sources
Beta strandi225 – 2317Combined sources
Beta strandi235 – 2384Combined sources
Beta strandi241 – 2477Combined sources
Turni248 – 2514Combined sources
Beta strandi253 – 2564Combined sources
Turni257 – 2604Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1EP1X-ray2.20B2-262[»]
1EP2X-ray2.40B2-262[»]
1EP3X-ray2.10B1-262[»]
ProteinModelPortaliP56968.
SMRiP56968. Positions 2-262.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP56968.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini3 – 104102FAD-binding FR-typeAdd
BLAST

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.
OrthoDBiEOG6RNQC2.

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.
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
EntryMethodResolution (Å)ChainPositionsPDBsum
1EP1X-ray2.20B2-262[»]
1EP2X-ray2.40B2-262[»]
1EP3X-ray2.10B1-262[»]
ProteinModelPortaliP56968.
SMRiP56968. Positions 2-262.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiP56968. 1 interaction.
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.
OrthoDBiEOG6RNQC2.

Enzyme and pathway databases

UniPathwayiUPA00070; UER00945.
BioCyciLLAC416870:GCDT-1131-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP56968.

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.
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...

Publicationsi

« Hide 'large scale' publications
  1. "Sequence analysis and identification of the pyrKDbF operon from Lactococcus lactis including a novel gene, pyrK, involved in pyrimidine biosynthesis."
    Andersen P.S., Martinussen J., Hammer K.
    J. Bacteriol. 178:5005-5012(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "The complete genome sequence of the lactic acid bacterial paradigm Lactococcus lactis subsp. cremoris MG1363."
    Wegmann U., O'Connell-Motherway M., Zomer A., Buist G., Shearman C., Canchaya C., Ventura M., Goesmann A., Gasson M.J., Kuipers O.P., van Sinderen D., Kok J.
    J. Bacteriol. 189:3256-3270(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: MG1363.
  3. "The B form of dihydroorotate dehydrogenase from Lactococcus lactis consists of two different subunits, encoded by the pyrDb and pyrK genes, and contains FMN, FAD, and [FeS] redox centers."
    Nielsen F.S., Andersen P.S., Jensen K.F.
    J. Biol. Chem. 271:29359-29365(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, COFACTOR, SUBUNIT.
  4. "Structure of dihydroorotate dehydrogenase B: electron transfer between two flavin groups bridged by an iron-sulphur cluster."
    Rowland P., Noerager S., Jensen K.F., Larsen S.
    Structure 8:1227-1238(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) IN COMPLEXES WITH FAD AND IRON-SULFUR, COFACTOR, REACTION MECHANISM.

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 11, 2015
This is version 109 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.