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Q5YPA6 (MEND_NOCFA) Reviewed, UniProtKB/Swiss-Prot

Last modified June 11, 2014. Version 68. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase

Short name=SEPHCHC synthase
EC=2.2.1.9
Alternative name(s):
Menaquinone biosynthesis protein MenD
Gene names
Name:menD
Ordered Locus Names:NFA_51330
OrganismNocardia farcinica (strain IFM 10152) [Complete proteome] [HAMAP]
Taxonomic identifier247156 [NCBI]
Taxonomic lineageBacteriaActinobacteriaActinobacteridaeActinomycetalesCorynebacterineaeNocardiaceaeNocardia

Protein attributes

Sequence length545 AA.
Sequence statusComplete.
Protein existenceInferred from homology

General annotation (Comments)

Function

Catalyzes the thiamine diphosphate-dependent decarboxylation of 2-oxoglutarate and the subsequent addition of the resulting succinic semialdehyde-thiamine pyrophosphate anion to isochorismate to yield 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate (SEPHCHC) By similarity. HAMAP-Rule MF_01659

Catalytic activity

Isochorismate + 2-oxoglutarate = 5-enolpyruvoyl-6-hydroxy-2-succinyl-cyclohex-3-ene-1-carboxylate + CO2. HAMAP-Rule MF_01659

Cofactor

Magnesium or manganese By similarity. HAMAP-Rule MF_01659

Binds 1 thiamine pyrophosphate per subunit By similarity.

Pathway

Cofactor biosynthesis; menaquinone biosynthesis; menaquinone-2 from chorismate: step 2/8. HAMAP-Rule MF_01659

Subunit structure

Homodimer By similarity. HAMAP-Rule MF_01659

Sequence similarities

Belongs to the TPP enzyme family. MenD subfamily.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 5455452-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase HAMAP-Rule MF_01659
PRO_0000341790

Sequences

Sequence LengthMass (Da)Tools
Q5YPA6 [UniParc].

Last modified November 23, 2004. Version 1.
Checksum: FB1DA1B4E63A4696

FASTA54556,577
        10         20         30         40         50         60 
MNPSTAQARV VVDELVRGGV RDVVLCPGSR NAPLAFALQA ADAAGRLRLH MRIDERTAGF 

        70         80         90        100        110        120 
LAIGLAISAG APVPVVMTSG TAVANLGPAV LEANYARVPL IVLSANRPYE MLGTGANQTV 

       130        140        150        160        170        180 
EQLGLFGSQV RATISLGLAE ADGAGAGSYD QQNSVWRSAV CRVLAAARGT RSGNAGPVHF 

       190        200        210        220        230        240 
DIPLREPLVP DLAEGEAEPA GRAGGAPWTA TQYATLDVPL EIDLTPDTVV VSGHGAGLRP 

       250        260        270        280        290        300 
ELAHLPTVAE PTAPMHGPAL HPLALPLLTP RQAIITGRPT LHRQVSRLLA DPAVTVYALT 

       310        320        330        340        350        360 
TGPRWPDVSG NVVGTGTRAV TSGGPRPEWL AHCRELDEKA RQVVRAELAG HPKPTGLHVA 

       370        380        390        400        410        420 
AVVMDALREG DQLLLGASNP VRDAALVATP RPGVRVLSNR GVAGIDGTVS TAVGAALAHP 

       430        440        450        460        470        480 
GRTIALIGDL TFLHDAAGLL IGRGEPRPAD LTIVVANDDG GGIFELLEQG DPQYAGVFER 

       490        500        510        520        530        540 
VFGTPHGMDL AALCAAYRIP HRQVDPAELA AELAGDAHGL RVLEVITERS SLRELHATVR 


AKIAP 

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References

[1]"The complete genomic sequence of Nocardia farcinica IFM 10152."
Ishikawa J., Yamashita A., Mikami Y., Hoshino Y., Kurita H., Hotta K., Shiba T., Hattori M.
Proc. Natl. Acad. Sci. U.S.A. 101:14925-14930(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: IFM 10152.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AP006618 Genomic DNA. Translation: BAD59985.1.
RefSeqYP_121349.1. NC_006361.1.

3D structure databases

ProteinModelPortalQ5YPA6.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING247156.nfa51330.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaBAD59985; BAD59985; NFA_51330.
GeneID3111276.
KEGGnfa:nfa51330.
PATRIC22739847. VBINocFar94200_5142.

Organism-specific databases

CMRSearch...

Phylogenomic databases

eggNOGCOG1165.
KOK02551.
OMAWRSAVCR.
OrthoDBEOG6NWBQW.

Enzyme and pathway databases

BioCycNFAR247156:GJ9T-5204-MONOMER.
UniPathwayUPA00079; UER00164.

Family and domain databases

Gene3D3.40.50.970. 2 hits.
HAMAPMF_01659. MenD.
InterProIPR004433. MenaQ_synth_MenD.
IPR029061. THDP-binding.
IPR012001. Thiamin_PyroP_enz_TPP-bd_dom.
IPR011766. TPP_enzyme-bd_C.
[Graphical view]
PfamPF02775. TPP_enzyme_C. 1 hit.
PF02776. TPP_enzyme_N. 1 hit.
[Graphical view]
PIRSFPIRSF004983. MenD. 1 hit.
SUPFAMSSF52518. SSF52518. 2 hits.
TIGRFAMsTIGR00173. menD. 1 hit.
ProtoNetSearch...

Entry information

Entry nameMEND_NOCFA
AccessionPrimary (citable) accession number: Q5YPA6
Entry history
Integrated into UniProtKB/Swiss-Prot: July 1, 2008
Last sequence update: November 23, 2004
Last modified: June 11, 2014
This is version 68 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PATHWAY comments

Index of metabolic and biosynthesis pathways