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Protein

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

Gene

menD

Organism
Clavibacter michiganensis subsp. sepedonicus (strain ATCC 33113 / DSM 20744 / JCM 9667 / LMG 2889 / C-1) (Corynebacterium sepedonicum)
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

Pathway: 1,4-dihydroxy-2-naphthoate biosynthesis

This protein is involved in step 2 of the subpathway that synthesizes 1,4-dihydroxy-2-naphthoate from chorismate.UniRule annotation
Proteins known to be involved in the 7 steps of the subpathway in this organism are:
  1. no protein annotated in this organism
  2. 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase (menD)
  3. no protein annotated in this organism
  4. o-succinylbenzoate synthase (menC)
  5. no protein annotated in this organism
  6. 1,4-dihydroxy-2-naphthoyl-CoA synthase (menB)
  7. no protein annotated in this organism
This subpathway is part of the pathway 1,4-dihydroxy-2-naphthoate biosynthesis, which is itself part of Quinol/quinone metabolism.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes 1,4-dihydroxy-2-naphthoate from chorismate, the pathway 1,4-dihydroxy-2-naphthoate biosynthesis and in Quinol/quinone metabolism.

Pathway: menaquinone biosynthesis

This protein is involved in the pathway menaquinone biosynthesis, which is part of Quinol/quinone metabolism.UniRule annotation
View all proteins of this organism that are known to be involved in the pathway menaquinone biosynthesis and in Quinol/quinone metabolism.

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Transferase

Keywords - Biological processi

Menaquinone biosynthesis

Keywords - Ligandi

Magnesium, Manganese, Metal-binding, Thiamine pyrophosphate

Enzyme and pathway databases

BioCyciCMIC31964:GJBN-3011-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:CMS3017
OrganismiClavibacter michiganensis subsp. sepedonicus (strain ATCC 33113 / DSM 20744 / JCM 9667 / LMG 2889 / C-1) (Corynebacterium sepedonicum)
Taxonomic identifieri31964 [NCBI]
Taxonomic lineageiBacteriaActinobacteriaMicrococcalesMicrobacteriaceaeClavibacter
ProteomesiUP000001318 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 5895892-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthasePRO_0000341725Add
BLAST

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi31964.CMS_3017.

Structurei

3D structure databases

ProteinModelPortaliB0RCZ5.
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.

B0RCZ5-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAAADALPTS SASASASADG PRTGNPSTDR AIAMLLALVR EGVTDVVLCP
60 70 80 90 100
GSRSQALALV AAELERVDGV RLHVRIDERA AGFLALGLGV ESGRPAPVIT
110 120 130 140 150
TSGTAVANLH PAVLEGWHSG VPMLLLTGDR PAELRGIASN QTTRQPGMFG
160 170 180 190 200
DRVACIDVPA PEETDDDLAR DALLARDAYR RARDERTPVH VNVAFRDPLS
210 220 230 240 250
VAVPDLTEAV AEVRAAAPAT PAPAGPATAD VLDLPHGPRT LVVAGHAAGE
260 270 280 290 300
AAEELARAGG WPLAAEISSG SHFGPNLVVS FRELLAREGF GDRVERVIVF
310 320 330 340 350
GHPTLTREVP LLVGREDVEA IVVGSTGGED YDPRHRVTAH PAAVRVVGEP
360 370 380 390 400
ADPAEARRWL GTWVHESRAI LDEATAAESA PLLPSGTTPA ERRDFARAEL
410 420 430 440 450
AAVRADVTRR HLVRALWQAT WPHDRLVLGA SRLIREADRA LPGKRVRVHA
460 470 480 490 500
NRGLAGIDGT ISTGLGIALA SQAGSGSAAA GITRVLVGDL TLLHDVGSLL
510 520 530 540 550
IGTGERVPRI QVIVGNDGGG TIFDGLEVSR TAAPASIDRV MFTPQRVDLA
560 570 580
SLARAYGWAH LRAATHGELE AALTTASEAP LLIEVPLAR
Length:589
Mass (Da):61,555
Last modified:April 8, 2008 - v1
Checksum:i82920B3D1DDA1B78
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AM849034 Genomic DNA. Translation: CAQ03087.1.
RefSeqiWP_012300234.1. NC_010407.1.
YP_001711643.1. NC_010407.1.

Genome annotation databases

EnsemblBacteriaiCAQ03087; CAQ03087; CMS3017.
KEGGicms:CMS_3017.
PATRICi21463057. VBIClaMic4666_3062.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AM849034 Genomic DNA. Translation: CAQ03087.1.
RefSeqiWP_012300234.1. NC_010407.1.
YP_001711643.1. NC_010407.1.

3D structure databases

ProteinModelPortaliB0RCZ5.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi31964.CMS_3017.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAQ03087; CAQ03087; CMS3017.
KEGGicms:CMS_3017.
PATRICi21463057. VBIClaMic4666_3062.

Phylogenomic databases

eggNOGiCOG1165.
KOiK02551.
OMAiWRSAVCR.
OrthoDBiEOG6NWBQW.

Enzyme and pathway databases

UniPathwayiUPA00079.
UPA01057; UER00164.
BioCyciCMIC31964:GJBN-3011-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. "Genome of the actinomycete plant pathogen Clavibacter michiganensis subsp. sepedonicus suggests recent niche adaptation."
    Bentley S.D., Corton C., Brown S.E., Barron A., Clark L., Doggett J., Harris B., Ormond D., Quail M.A., May G., Francis D., Knudson D., Parkhill J., Ishimaru C.A.
    J. Bacteriol. 190:2150-2160(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 33113 / DSM 20744 / JCM 9667 / LMG 2889 / C-1.

Entry informationi

Entry nameiMEND_CLAMS
AccessioniPrimary (citable) accession number: B0RCZ5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 1, 2008
Last sequence update: April 8, 2008
Last modified: June 24, 2015
This is version 57 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.