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Protein

2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase

Gene

menD

Organism
Nocardia farcinica (strain IFM 10152)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

Functioni

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).UniRule annotation

Catalytic activityi

Isochorismate + 2-oxoglutarate = 5-enolpyruvoyl-6-hydroxy-2-succinyl-cyclohex-3-ene-1-carboxylate + CO2.UniRule annotation

Cofactori

Protein has several cofactor binding sites:
  • Mg2+UniRule annotation, Mn2+UniRule annotation
  • thiamine diphosphateUniRule annotationNote: Binds 1 thiamine pyrophosphate per subunit.UniRule annotation

Pathwayi

GO - Molecular functioni

  1. 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase activity Source: UniProtKB-HAMAP
  2. magnesium ion binding Source: UniProtKB-HAMAP
  3. manganese ion binding Source: UniProtKB-HAMAP
  4. thiamine pyrophosphate binding Source: UniProtKB-HAMAP

GO - Biological processi

  1. menaquinone biosynthetic process Source: UniProtKB-HAMAP
Complete GO annotation...

Keywords - Molecular functioni

Transferase

Keywords - Biological processi

Menaquinone biosynthesis

Keywords - Ligandi

Magnesium, Manganese, Metal-binding, Thiamine pyrophosphate

Enzyme and pathway databases

BioCyciNFAR247156:GJ9T-5204-MONOMER.
UniPathwayiUPA00079.
UPA01057; UER00164.

Names & Taxonomyi

Protein namesi
Recommended name:
2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthaseUniRule annotation (EC:2.2.1.9UniRule annotation)
Short name:
SEPHCHC synthaseUniRule annotation
Alternative name(s):
Menaquinone biosynthesis protein MenDUniRule annotation
Gene namesi
Name:menDUniRule annotation
Ordered Locus Names:NFA_51330
OrganismiNocardia farcinica (strain IFM 10152)
Taxonomic identifieri247156 [NCBI]
Taxonomic lineageiBacteriaActinobacteriaActinobacteridaeActinomycetalesCorynebacterineaeNocardiaceaeNocardia
ProteomesiUP000006820 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 5455452-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthasePRO_0000341790Add
BLAST

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi247156.nfa51330.

Structurei

3D structure databases

ProteinModelPortaliQ5YPA6.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the TPP enzyme family. MenD subfamily.UniRule annotation

Phylogenomic databases

eggNOGiCOG1165.
KOiK02551.
OMAiWRSAVCR.
OrthoDBiEOG6NWBQW.

Family and domain databases

Gene3Di3.40.50.970. 2 hits.
HAMAPiMF_01659. MenD.
InterProiIPR004433. MenaQ_synth_MenD.
IPR029061. THDP-binding.
IPR012001. Thiamin_PyroP_enz_TPP-bd_dom.
IPR011766. TPP_enzyme-bd_C.
[Graphical view]
PfamiPF02775. TPP_enzyme_C. 1 hit.
PF02776. TPP_enzyme_N. 1 hit.
[Graphical view]
PIRSFiPIRSF004983. MenD. 1 hit.
SUPFAMiSSF52518. SSF52518. 2 hits.
TIGRFAMsiTIGR00173. menD. 1 hit.

Sequencei

Sequence statusi: Complete.

Q5YPA6-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MNPSTAQARV VVDELVRGGV RDVVLCPGSR NAPLAFALQA ADAAGRLRLH
60 70 80 90 100
MRIDERTAGF LAIGLAISAG APVPVVMTSG TAVANLGPAV LEANYARVPL
110 120 130 140 150
IVLSANRPYE MLGTGANQTV EQLGLFGSQV RATISLGLAE ADGAGAGSYD
160 170 180 190 200
QQNSVWRSAV CRVLAAARGT RSGNAGPVHF DIPLREPLVP DLAEGEAEPA
210 220 230 240 250
GRAGGAPWTA TQYATLDVPL EIDLTPDTVV VSGHGAGLRP ELAHLPTVAE
260 270 280 290 300
PTAPMHGPAL HPLALPLLTP RQAIITGRPT LHRQVSRLLA DPAVTVYALT
310 320 330 340 350
TGPRWPDVSG NVVGTGTRAV TSGGPRPEWL AHCRELDEKA RQVVRAELAG
360 370 380 390 400
HPKPTGLHVA AVVMDALREG DQLLLGASNP VRDAALVATP RPGVRVLSNR
410 420 430 440 450
GVAGIDGTVS TAVGAALAHP GRTIALIGDL TFLHDAAGLL IGRGEPRPAD
460 470 480 490 500
LTIVVANDDG GGIFELLEQG DPQYAGVFER VFGTPHGMDL AALCAAYRIP
510 520 530 540
HRQVDPAELA AELAGDAHGL RVLEVITERS SLRELHATVR AKIAP
Length:545
Mass (Da):56,577
Last modified:November 23, 2004 - v1
Checksum:iFB1DA1B4E63A4696
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP006618 Genomic DNA. Translation: BAD59985.1.
RefSeqiYP_121349.1. NC_006361.1.

Genome annotation databases

EnsemblBacteriaiBAD59985; BAD59985; NFA_51330.
KEGGinfa:nfa51330.
PATRICi22739847. VBINocFar94200_5142.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP006618 Genomic DNA. Translation: BAD59985.1.
RefSeqiYP_121349.1. NC_006361.1.

3D structure databases

ProteinModelPortaliQ5YPA6.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi247156.nfa51330.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAD59985; BAD59985; NFA_51330.
KEGGinfa:nfa51330.
PATRICi22739847. VBINocFar94200_5142.

Phylogenomic databases

eggNOGiCOG1165.
KOiK02551.
OMAiWRSAVCR.
OrthoDBiEOG6NWBQW.

Enzyme and pathway databases

UniPathwayiUPA00079.
UPA01057; UER00164.
BioCyciNFAR247156:GJ9T-5204-MONOMER.

Family and domain databases

Gene3Di3.40.50.970. 2 hits.
HAMAPiMF_01659. MenD.
InterProiIPR004433. MenaQ_synth_MenD.
IPR029061. THDP-binding.
IPR012001. Thiamin_PyroP_enz_TPP-bd_dom.
IPR011766. TPP_enzyme-bd_C.
[Graphical view]
PfamiPF02775. TPP_enzyme_C. 1 hit.
PF02776. TPP_enzyme_N. 1 hit.
[Graphical view]
PIRSFiPIRSF004983. MenD. 1 hit.
SUPFAMiSSF52518. SSF52518. 2 hits.
TIGRFAMsiTIGR00173. menD. 1 hit.
ProtoNetiSearch...

Publicationsi

  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: IFM 10152.

Entry informationi

Entry nameiMEND_NOCFA
AccessioniPrimary (citable) accession number: Q5YPA6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 1, 2008
Last sequence update: November 23, 2004
Last modified: April 1, 2015
This is version 75 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

Complete proteome, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.