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Protein

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

Gene

menD

Organism
Prosthecochloris aestuarii (strain DSM 271 / SK 413)
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: 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. Putative 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase (menH)
  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.

Pathwayi: 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

BioCyciPAES290512:GHUT-1926-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:Paes_1878
OrganismiProsthecochloris aestuarii (strain DSM 271 / SK 413)
Taxonomic identifieri290512 [NCBI]
Taxonomic lineageiBacteriaChlorobiChlorobiaChlorobialesChlorobiaceaeProsthecochloris
Proteomesi
  • UP000002725 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 5785782-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthasePRO_1000187085Add
BLAST

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi290512.Paes_1878.

Structurei

3D structure databases

ProteinModelPortaliB4S4J4.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiENOG4105C4A. Bacteria.
COG1165. LUCA.
HOGENOMiHOG000218359.
KOiK02551.
OMAiIFRILPG.
OrthoDBiEOG6NWBQW.

Family and domain databases

Gene3Di3.40.50.1220. 1 hit.
3.40.50.970. 2 hits.
HAMAPiMF_01659. MenD.
InterProiIPR029035. DHS-like_NAD/FAD-binding_dom.
IPR004433. MenaQ_synth_MenD.
IPR032264. MenD_middle.
IPR029061. THDP-binding.
IPR012001. Thiamin_PyroP_enz_TPP-bd_dom.
IPR011766. TPP_enzyme-bd_C.
[Graphical view]
PfamiPF02775. TPP_enzyme_C. 1 hit.
PF16582. TPP_enzyme_M_2. 1 hit.
PF02776. TPP_enzyme_N. 1 hit.
[Graphical view]
PIRSFiPIRSF004983. MenD. 1 hit.
SUPFAMiSSF52467. SSF52467. 2 hits.
SSF52518. SSF52518. 2 hits.
TIGRFAMsiTIGR00173. menD. 1 hit.

Sequencei

Sequence statusi: Complete.

B4S4J4-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MNHKEITTLW SWIIVEELVR NSICFFCISP GSRSTPLTVA ASRHQKTTCK
60 70 80 90 100
IFPDERAAAF FALGYARATG RPAVLICTSG TAAANYFPAV VEASMGHQPM
110 120 130 140 150
LVLSADRPFE LRETGANQTI RQSGIYGSYS RWSFQLPEPS TDTPPEAILS
160 170 180 190 200
AIDYAVSTCT ANPSGPVHLN IAFREPLEPV PLNENSPWLS SLGKWNSSRA
210 220 230 240 250
PWSRTLQRQS SPESASVKEV ARLLASAENP LIIAGHLDRP ADAQAVLNLS
260 270 280 290 300
KSLNIALYAD ISSQLRLHKE TVALQQAWLS DKYVEQHRAD LVLHFGGSLV
310 320 330 340 350
GKKPGQAMKT WRPDHTIVIK NHPDRYAPDH TVTMSIEASV KAFAEALAKT
360 370 380 390 400
SQPQGKKANP IDEIEQEIER FTRPDSPVTE ISAARIVSRL IDPGHGLFLA
410 420 430 440 450
NSMPVRDMDM YATRSGGTII PTAMNRGASG IDGIISSAAG FASGLERPVT
460 470 480 490 500
LLIGDISFLH DMNALCLLRS MTVPLTIVVI NNNGGGIFSF LPISDQPDVF
510 520 530 540 550
EKNFGTPQEF NIAAAATAFS IEYQCPPSNA AFSESYMAAR SSAETSIIEI
560 570
RSRRDENLAL HRKLNQSLID RLDRQQSC
Length:578
Mass (Da):63,153
Last modified:September 23, 2008 - v1
Checksum:i235764D7C81A1966
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001108 Genomic DNA. Translation: ACF46890.1.
RefSeqiWP_012506423.1. NC_011059.1.

Genome annotation databases

EnsemblBacteriaiACF46890; ACF46890; Paes_1878.
KEGGipaa:Paes_1878.
PATRICi23043668. VBIProAes37017_1999.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001108 Genomic DNA. Translation: ACF46890.1.
RefSeqiWP_012506423.1. NC_011059.1.

3D structure databases

ProteinModelPortaliB4S4J4.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi290512.Paes_1878.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiACF46890; ACF46890; Paes_1878.
KEGGipaa:Paes_1878.
PATRICi23043668. VBIProAes37017_1999.

Phylogenomic databases

eggNOGiENOG4105C4A. Bacteria.
COG1165. LUCA.
HOGENOMiHOG000218359.
KOiK02551.
OMAiIFRILPG.
OrthoDBiEOG6NWBQW.

Enzyme and pathway databases

UniPathwayiUPA00079.
UPA01057; UER00164.
BioCyciPAES290512:GHUT-1926-MONOMER.

Family and domain databases

Gene3Di3.40.50.1220. 1 hit.
3.40.50.970. 2 hits.
HAMAPiMF_01659. MenD.
InterProiIPR029035. DHS-like_NAD/FAD-binding_dom.
IPR004433. MenaQ_synth_MenD.
IPR032264. MenD_middle.
IPR029061. THDP-binding.
IPR012001. Thiamin_PyroP_enz_TPP-bd_dom.
IPR011766. TPP_enzyme-bd_C.
[Graphical view]
PfamiPF02775. TPP_enzyme_C. 1 hit.
PF16582. TPP_enzyme_M_2. 1 hit.
PF02776. TPP_enzyme_N. 1 hit.
[Graphical view]
PIRSFiPIRSF004983. MenD. 1 hit.
SUPFAMiSSF52467. SSF52467. 2 hits.
SSF52518. SSF52518. 2 hits.
TIGRFAMsiTIGR00173. menD. 1 hit.
ProtoNetiSearch...

Publicationsi

  1. "Complete sequence of chromosome of Prosthecochloris aestuarii DSM 271."
    US DOE Joint Genome Institute
    Lucas S., Copeland A., Lapidus A., Glavina del Rio T., Dalin E., Tice H., Bruce D., Goodwin L., Pitluck S., Schmutz J., Larimer F., Land M., Hauser L., Kyrpides N., Anderson I., Liu Z., Li T., Zhao F.
    , Overmann J., Bryant D.A., Richardson P.
    Submitted (JUN-2008) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: DSM 271 / SK 413.

Entry informationi

Entry nameiMEND_PROA2
AccessioniPrimary (citable) accession number: B4S4J4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 28, 2009
Last sequence update: September 23, 2008
Last modified: November 11, 2015
This is version 56 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

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 one 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.