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Protein

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

Gene

menD

Organism
Clavibacter michiganensis subsp. michiganensis (strain NCPPB 382)
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

BioCyciCMIC443906:GCI2-2898-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:CMM_2812
OrganismiClavibacter michiganensis subsp. michiganensis (strain NCPPB 382)
Taxonomic identifieri443906 [NCBI]
Taxonomic lineageiBacteriaActinobacteriaMicrococcalesMicrobacteriaceaeClavibacter
ProteomesiUP000001564 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 5885882-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthasePRO_0000341724Add
BLAST

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi443906.CMM_2812.

Structurei

3D structure databases

ProteinModelPortaliA5CUV9.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiCOG1165.
HOGENOMiHOG000218359.
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.

A5CUV9-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTTTGSLPAQ PSSTSPRTGN PSTDRALAML LALVREGVTD VVLCPGSRSQ
60 70 80 90 100
ALALVAAELE RVDGVRLHVR IDERAAGFLA LGLGVESGRP APVITTSGTA
110 120 130 140 150
VANLHPAVLE GWHSGVPMLL LTGDRPAELR GIASNQTTRQ PGMFGDRVVV
160 170 180 190 200
VDVPAPEETD EDLSRDARLA RDAYRRARDE RTPVHVNVAF RDPLSVAVPD
210 220 230 240 250
LAEAVAEAHA AADAEAAAAP APAGPTAADV LDLPHGPRTL VVAGHAAGEA
260 270 280 290 300
AEELARAGGW PLAAEISSGS HFGPNLVVSF RELLARPGFG DRVERVIVFG
310 320 330 340 350
HPTLTREVPL LVGREDVEAI VVGSTGGEDY DPRHRVTAHP AAVRVVGEPA
360 370 380 390 400
DPAEARRWTG TWVQASRAIL DEASAAESAP LLPSGTTPAE RRDFARAELA
410 420 430 440 450
AVRADVTRRH LVRALWQATW PHDRLVLGAS RLIREADRAL PGKRVRVHAN
460 470 480 490 500
RGLAGIDGTI STGLGIALAS QAGSGSAAAG ITRVLVGDLT LLHDVGSLLI
510 520 530 540 550
GTGERVPRIQ VIVGNDGGGT IFDGLEVANT AAPAAIDRVM FTPQRVDLAS
560 570 580
LAKAYGWTHL RAATHGELEA ALTTASGAPL LIEVPLVR
Length:588
Mass (Da):61,363
Last modified:June 12, 2007 - v1
Checksum:i52D8F8F15A9CB078
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AM711867 Genomic DNA. Translation: CAN02897.1.
RefSeqiWP_012039500.1. NC_009480.1.
YP_001223557.1. NC_009480.1.

Genome annotation databases

EnsemblBacteriaiCAN02897; CAN02897; CMM_2812.
KEGGicmi:CMM_2812.
PATRICi21456487. VBIClaMic82482_2937.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AM711867 Genomic DNA. Translation: CAN02897.1.
RefSeqiWP_012039500.1. NC_009480.1.
YP_001223557.1. NC_009480.1.

3D structure databases

ProteinModelPortaliA5CUV9.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi443906.CMM_2812.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAN02897; CAN02897; CMM_2812.
KEGGicmi:CMM_2812.
PATRICi21456487. VBIClaMic82482_2937.

Phylogenomic databases

eggNOGiCOG1165.
HOGENOMiHOG000218359.
KOiK02551.
OMAiWRSAVCR.
OrthoDBiEOG6NWBQW.

Enzyme and pathway databases

UniPathwayiUPA00079.
UPA01057; UER00164.
BioCyciCMIC443906:GCI2-2898-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. "The genome sequence of the tomato-pathogenic actinomycete Clavibacter michiganensis subsp. michiganensis NCPPB382 reveals a large island involved in pathogenicity."
    Gartemann K.-H., Abt B., Bekel T., Burger A., Engemann J., Fluegel M., Gaigalat L., Goesmann A., Graefen I., Kalinowski J., Kaup O., Kirchner O., Krause L., Linke B., McHardy A., Meyer F., Pohle S., Rueckert C.
    , Schneiker S., Zellermann E.-M., Puehler A., Eichenlaub R., Kaiser O., Bartels D.
    J. Bacteriol. 190:2138-2149(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: NCPPB 382.

Entry informationi

Entry nameiMEND_CLAM3
AccessioniPrimary (citable) accession number: A5CUV9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 1, 2008
Last sequence update: June 12, 2007
Last modified: June 24, 2015
This is version 63 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

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.