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menD 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase [ Escherichia coli str. K-12 substr. MG1655 ]

Gene ID: 946720, updated on 4-Apr-2024

Summary

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Gene symbol
menD
Gene description
2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
Primary source
ASAP:ABE-0007482
Locus tag
b2264
See related
ECOCYC:EG10579
Gene type
protein coding
RefSeq status
PROVISIONAL
Organism
Escherichia coli str. K-12 substr. MG1655 (strain: K-12, substrain: MG1655)
Lineage
Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Escherichia
Also known as
ECK2258
Summary
Mistakenly thought to be SHCHC synthase (Jiang, 2007). [More information is available at EcoGene: EG10579]. The menD gene product catalyzes the first committed step in the biosynthesis of menaquinone. [More information is available at EcoCyc: EG10579].
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Genomic context

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Sequence:
NC_000913.3 (2377589..2379259, complement)

NC_000913.3Genomic Context describing neighboring genes Neighboring gene o-succinylbenzoate--CoA ligase Neighboring gene o-succinylbenzoate synthase Neighboring gene 1,4-dihydroxy-2-naphthoyl-CoA synthase Neighboring gene 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase Neighboring gene isochorismate synthase MenF Neighboring gene tail-anchored inner membrane protein ElaB

Genomic regions, transcripts, and products

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Genomic Sequence:
NC_000913.3

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. Two active site arginines are critical determinants of substrate binding and catalysis in MenD: a thiamine-dependent enzyme in menaquinone biosynthesis. Qin M, et al. Biochem J, 2018 Nov 30. PMID 30341164
  2. New Stetter reactions catalyzed by thiamine diphosphate dependent MenD from E. coli. Beigi M, et al. J Biotechnol, 2014 Dec 10. PMID 25111035
  3. Using substrate analogues to probe the kinetic mechanism and active site of Escherichia coli MenD. Fang M, et al. Biochemistry, 2011 Oct 11. PMID 21928762
  4. Structural and functional analysis of Vitamin K2 synthesis protein MenD. Priyadarshi A, et al. Biochem Biophys Res Commun, 2009 Oct 30. PMID 19703421
  5. Structural insights of the MenD from Escherichia coli reveal ThDP affinity. Priyadarshi A, et al. Biochem Biophys Res Commun, 2009 Mar 20. PMID 19338755

See all (30) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. The non-native-binding site of the inactive 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexadiene-1-carboxylate synthase (MenD) intermediate suggests a target for the development of antibiotics.
    Title: Two active site arginines are critical determinants of substrate binding and catalysis in MenD: a thiamine-dependent enzyme in menaquinone biosynthesis.
  2. MenD possesses a characteristic substrate range with respect to Michael acceptor substrates which is distinctly different from the classical stetterases.
    Title: New Stetter reactions catalyzed by thiamine diphosphate dependent MenD from E. coli.
  3. The active-Site of MenD are Arg33, Arg107, Lys292, Arg293, Arg395, and Arg413.
    Title: Using substrate analogues to probe the kinetic mechanism and active site of Escherichia coli MenD.
  4. the crystal structures of the Vitamin K(2) synthesis protein MenD were described.
    Title: Structural and functional analysis of Vitamin K2 synthesis protein MenD.
  5. the crystal structure of apo MenD with supporting biological assay that reveals its affinity towards ThDP, FAD and oxoglutarate, providing further insight into its function and role as a bifunctional enzyme.
    Title: Structural insights of the MenD from Escherichia coli reveal ThDP affinity.
  6. The results showed that E. coli K12 carrying a deletion of either the menD, menC or menE gene was unable to reduce selenate.
    Title: Role of menaquinone biosynthesis genes in selenate reduction by Enterobacter cloacae SLD1a-1 and Escherichia coli K12.
Submit: New GeneRIF Correction

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Gene Ontology Provided by EcoCyc

Function Evidence Code Pubs
enables 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase activity IEA
Inferred from Electronic Annotation
more info
  
enables catalytic activity IEA
Inferred from Electronic Annotation
more info
  
enables magnesium ion binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables magnesium ion binding IEA
Inferred from Electronic Annotation
more info
  
enables manganese ion binding IEA
Inferred from Electronic Annotation
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables protein homodimerization activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables thiamine pyrophosphate binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables thiamine pyrophosphate binding IEA
Inferred from Electronic Annotation
more info
  
enables transferase activity IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in menaquinone biosynthetic process IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within menaquinone biosynthetic process IMP
Inferred from Mutant Phenotype
more info
 PubMed 

General protein information

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Preferred Names
2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
NP_416767.1

NCBI Reference Sequences (RefSeq)

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Genome Annotation

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference assembly

Genomic

  1. NC_000913.3 Reference assembly

    Range
    2377589..2379259 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NP_416767.1 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase [Escherichia coli str. K-12 substr. MG1655]

    See identical proteins and their annotated locations for NP_416767.1

    Status: PROVISIONAL

    UniProtKB/TrEMBL
    A0A6L6ZMG6, A0A8S7EBA5
    Conserved Domains (1) summary
    PRK07449
    Location:1 → 556
    PRK07449; 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase; Validated
Nucleotide Protein
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