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Protein

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

Gene

menD

Organism
Escherichia coli (strain K12 / DH10B)
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. 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase (menH)
  4. o-succinylbenzoate synthase (menC)
  5. no protein annotated in this organism
  6. no protein annotated in this organism
  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

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:ECDH10B_2425
OrganismiEscherichia coli (strain K12 / DH10B)
Taxonomic identifieri316385 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_10001870741 – 5562-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthaseAdd BLAST556

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi316385.ECDH10B_2425.

Structurei

3D structure databases

ProteinModelPortaliB1X8X8.
SMRiB1X8X8.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiENOG4105C4A. Bacteria.
COG1165. LUCA.
HOGENOMiHOG000218360.
KOiK02551.
OMAiIFRILPG.

Family and domain databases

Gene3Di3.40.50.970. 2 hits.
HAMAPiMF_01659. MenD. 1 hit.
InterProiIPR004433. 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.
SUPFAMiSSF52518. SSF52518. 2 hits.
TIGRFAMsiTIGR00173. menD. 1 hit.

Sequencei

Sequence statusi: Complete.

B1X8X8-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSVSAFNRRW AAVILEALTR HGVRHICIAP GSRSTPLTLA AAENSAFIHH
60 70 80 90 100
THFDERGLGH LALGLAKVSK QPVAVIVTSG TAVANLYPAL IEAGLTGEKL
110 120 130 140 150
ILLTADRPPE LIDCGANQAI RQPGMFASHP THSISLPRPT QDIPARWLVS
160 170 180 190 200
TIDHALGTLH AGGVHINCPF AEPLYGEMDD TGLSWQQRLG DWWQDDKPWL
210 220 230 240 250
REAPRLESEK QRDWFFWRQK RGVVVAGRMS AEEGKKVALW AQTLGWPLIG
260 270 280 290 300
DVLSQTGQPL PCADLWLGNA KATSELQQAQ IVVQLGSSLT GKRLLQWQAS
310 320 330 340 350
CEPEEYWIVD DIEGRLDPAH HRGRRLIANI ADWLELHPAE KRQPWCVEIP
360 370 380 390 400
RLAEQAMQAV IARRDAFGEA QLAHRICDYL PEQGQLFVGN SLVVRLIDAL
410 420 430 440 450
SQLPAGYPVY SNRGASGIDG LLSTAAGVQR ASGKPTLAIV GDLSALYDLN
460 470 480 490 500
ALALLRQVSA PLVLIVVNNN GGQIFSLLPT PQSERERFYL MPQNVHFEHA
510 520 530 540 550
AAMFELKYHR PQNWQELETA FADAWRTPTT TVIEMVVNDT DGAQTLQQLL

AQVSHL
Length:556
Mass (Da):61,367
Last modified:May 20, 2008 - v1
Checksum:i278201D02243E76D
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000948 Genomic DNA. Translation: ACB03425.1.
RefSeqiWP_001295284.1. NC_010473.1.

Genome annotation databases

EnsemblBacteriaiACB03425; ACB03425; ECDH10B_2425.
KEGGiecd:ECDH10B_2425.
PATRICi18464721. VBIEscCol59506_2447.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000948 Genomic DNA. Translation: ACB03425.1.
RefSeqiWP_001295284.1. NC_010473.1.

3D structure databases

ProteinModelPortaliB1X8X8.
SMRiB1X8X8.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi316385.ECDH10B_2425.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiACB03425; ACB03425; ECDH10B_2425.
KEGGiecd:ECDH10B_2425.
PATRICi18464721. VBIEscCol59506_2447.

Phylogenomic databases

eggNOGiENOG4105C4A. Bacteria.
COG1165. LUCA.
HOGENOMiHOG000218360.
KOiK02551.
OMAiIFRILPG.

Enzyme and pathway databases

UniPathwayiUPA00079.
UPA01057; UER00164.

Family and domain databases

Gene3Di3.40.50.970. 2 hits.
HAMAPiMF_01659. MenD. 1 hit.
InterProiIPR004433. 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.
SUPFAMiSSF52518. SSF52518. 2 hits.
TIGRFAMsiTIGR00173. menD. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiMEND_ECODH
AccessioniPrimary (citable) accession number: B1X8X8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 28, 2009
Last sequence update: May 20, 2008
Last modified: November 2, 2016
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

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.