Q5YPA6 (MEND_NOCFA) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended 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

Organism

Nocardia farcinica (strain IFM 10152) [Complete proteome] [HAMAP]

Taxonomic identifier

247156 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Actinobacteria › Actinobacteria › Actinobacteridae › Actinomycetales › Corynebacterineae › Nocardiaceae › Nocardia › Nocardia farcinica

Protein attributes

Sequence length	545 AA.
Sequence status	Complete.
Protein existence	Inferred 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. 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.
Sequence similarities	Belongs to the TPP enzyme family. MenD subfamily.

Ontologies

Keywords
Biological process	Menaquinone biosynthesis
Ligand	Magnesium Manganese Metal-binding Thiamine pyrophosphate
Molecular function	Transferase
Technical term	Complete proteome
Gene Ontology (GO)
Biological_process	menaquinone biosynthetic process Inferred from electronic annotation. Source: HAMAP
Molecular_function	2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase activity Inferred from electronic annotation. Source: EC magnesium ion binding Inferred from electronic annotation. Source: HAMAP manganese ion binding Inferred from electronic annotation. Source: HAMAP thiamine pyrophosphate binding Inferred from electronic annotation. Source: HAMAP
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 545	545	2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase HAMAP-Rule MF_01659		PRO_0000341790

Sequences

	Sequence		Length	Mass (Da)
	Q5YPA6 [UniParc]. Last modified November 23, 2004. Version 1. Checksum: FB1DA1B4E63A4696	FASTA	545	56,577
	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

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.
RefSeq	YP_121349.1. NC_006361.1.
3D structure databases
ProteinModelPortal	Q5YPA6.
ModBase	Search...
Protein-protein interaction databases
STRING	247156.nfa51330.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblBacteria	BAD59985; BAD59985; NFA_51330.
GeneID	3111276.
KEGG	nfa:nfa51330.
PATRIC	22739847. VBINocFar94200_5142.
Organism-specific databases
CMR	Search...
Phylogenomic databases
eggNOG	COG1165.
KO	K02551.
OMA	ANRPYEM.
ProtClustDB	PRK07449.
Enzyme and pathway databases
BioCyc	NFAR247156:GJ9T-5204-MONOMER.
UniPathway	UPA00079; UER00164.
Family and domain databases
HAMAP	MF_01659. MenD.
InterPro	IPR004433. MenaQ_synth_MenD. IPR012001. Thiamin_PyroP_enz_TPP-bd_dom. IPR011766. TPP_enzyme-bd_C. [Graphical view]
PANTHER	PTHR18968:SF3. PTHR18968:SF3. 1 hit.
Pfam	PF02775. TPP_enzyme_C. 1 hit. PF02776. TPP_enzyme_N. 1 hit. [Graphical view]
PIRSF	PIRSF004983. MenD. 1 hit.
TIGRFAMs	TIGR00173. menD. 1 hit.
ProtoNet	Search...

Entry information

Entry name

MEND_NOCFA

Accession

Primary (citable) accession number: Q5YPA6

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 1, 2008
Last sequence update:	November 23, 2004
Last modified:	May 1, 2013
This is version 62 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program