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P56968 (PYRK_LACLM) Reviewed, UniProtKB/Swiss-Prot

Last modified January 25, 2012. Version 80. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
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Names and origin

Protein namesRecommended name:
Dihydroorotate dehydrogenase B (NAD(+)), electron transfer subunit
Alternative name(s):
Dihydrdoorotate oxidase B, electron transfer subunit
Gene names
Name:pyrK
Ordered Locus Names:llmg_1105
OrganismLactococcus lactis subsp. cremoris (strain MG1363) [Complete proteome] [HAMAP]
Taxonomic identifier416870 [NCBI]
Taxonomic lineageBacteria › Firmicutes › Lactobacillales › Streptococcaceae › Lactococcus

Protein attributes

Sequence length262 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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+. Ref.3

Cofactor

Binds 1 2Fe-2S cluster per subunit. Ref.3 Ref.4

Binds 1 FAD per subunit. Ref.3 Ref.4

Pathway

Pyrimidine metabolism; UMP biosynthesis via de novo pathway; orotate from (S)-dihydroorotate (NAD(+) route): step 1/1. HAMAP MF_01211

Subunit structure

Heterotetramer of 2 PyrK and 2 PyrD type B subunits. Ref.3

Subcellular location

Cytoplasm HAMAP MF_01211.

Sequence similarities

Belongs to the PyrK family.

Contains 1 FAD-binding FR-type domain.

Binary interactions

With

Entry

#Exp.

IntAct

Notes

pyrDBP543223EBI-1030589,EBI-1030598

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 262262Dihydroorotate dehydrogenase B (NAD(+)), electron transfer subunit HAMAP MF_01211
PRO_0000148363

Regions

Domain3 – 104102FAD-binding FR-type
Nucleotide binding53 – 564FAD HAMAP MF_01211
Nucleotide binding70 – 723FAD HAMAP MF_01211
Nucleotide binding79 – 802FAD HAMAP MF_01211

Sites

Metal binding2261Iron-sulfur (2Fe-2S)
Metal binding2311Iron-sulfur (2Fe-2S)
Metal binding2341Iron-sulfur (2Fe-2S)
Metal binding2491Iron-sulfur (2Fe-2S)

Secondary structure

1 .................................................. 262
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P56968 [UniParc].

Last modified December 1, 2000. Version 1.
Checksum: 9373DB3A75200DB3

FASTA26228,660
        10         20         30         40         50         60 
MSQLQEMMTV VSQREVAYNI FEMVLKGTLV DEMDLPGQFL HLAVPNGAML LRRPISISSW 

        70         80         90        100        110        120 
DKRAKTCTIL YRIGDETTGT YKLSKLESGA KVDVMGPLGN GFPVAEVTST DKILIIGGGI 

       130        140        150        160        170        180 
GVPPLYELAK QLEKTGCQMT ILLGFASENV KILENEFSNL KNVTLKIATD DGSYGTKGHV 

       190        200        210        220        230        240 
GMLMNEIDFE VDALYTCGAP AMLKAVAKKY DQLERLYISM ESRMACGIGA CYACVEHDKE 

       250        260 
DESHALKVCE DGPVFLGKQL SL

« Hide

References

« Hide 'large scale' references
[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: 8759867] [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: 17307855] [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: 8910599] [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: 11188687] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) IN COMPLEXES WITH FAD AND IRON-SULFUR, COFACTOR, REACTION MECHANISM.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		X74207 Genomic DNA. No translation available.
AM406671 Genomic DNA. Translation: CAL97699.1.
RefSeqYP_001032419.1. NC_009004.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1EP1X-ray2.20B2-262[»]
1EP2X-ray2.40B2-262[»]
1EP3X-ray2.10B1-262[»]
ProteinModelPortalP56968.
SMRP56968. Positions 2-262.
ModBaseSearch...

Protein-protein interaction databases

IntActP56968. 1 interaction.
MINTMINT-159270.
STRINGP56968.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

GeneID4797217.
GenomeReviewsGene locus llmg_1105 in contig AM406671_GR.
KEGGllm:llmg_1105.
PATRIC22283358. VBILacLac4574_1136.

Organism-specific databases

CMRSearch...

Phylogenomic databases

eggNOGCOG0543.
HOGENOMHBG730970.
OMARPISICS.
ProtClustDBCLSK697702.

Family and domain databases

HAMAPMF_01211. DHODB_Fe-S_bind.
[Tree]
InterProIPR012165. Cyt_c3_hydrogenase_gsu.
IPR019480. Dihydroorotate_DH_Fe-S-bd.
IPR023455. Dihydroorotate_DHASE_ETsu.
IPR017927. Fd_Rdtase_FAD-bd.
IPR008333. OxRdtase_FAD-bd_dom.
IPR001433. OxRdtase_FAD/NAD-bd.
IPR000951. Ph_dOase_redase.
IPR017938. Riboflavin_synthase-like_b-brl.
[Graphical view]
Gene3DG3DSA:2.10.240.10. G3DSA:2.10.240.10. 1 hit.
KOK02823.
PfamPF10418. DHODB_Fe-S_bind. 1 hit.
PF00970. FAD_binding_6. 1 hit.
PF00175. NAD_binding_1. 1 hit.
[Graphical view]
PIRSFPIRSF006816. Cyc3_hyd_g. 1 hit.
PRINTSPR00409. PHDIOXRDTASE.
SUPFAMSSF63380. Riboflavin_synthase_like_b-brl. 1 hit.
PROSITEPS51384. FAD_FR. 1 hit.
[Graphical view]
ProtoNetSearch...

Entry information

Entry namePYRK_LACLM
AccessionPrimary (citable) accession number: P56968
Secondary accession number(s): A2RK89
Entry history
Integrated into UniProtKB/Swiss-Prot: December 1, 2000
Last sequence update: December 1, 2000
Last modified: January 25, 2012
This is version 80 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

PATHWAY comments

Index of metabolic and biosynthesis pathways

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

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