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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 3-Dec-2024

    Summary

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    Official Symbol
    menD
    Official Full Name
    2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
    Primary source
    ECOCYC:EG10579
    Locus tag
    b2264
    See related
    ASAP:ABE-0007482
    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. New Stetter reactions catalyzed by thiamine diphosphate dependent MenD from E. coli. Beigi M, et al. J Biotechnol, 2014 Dec 10. PMID 25111035
    2. Enzymes from Escherichia coli synthesize o-succinylbenzoic acid, an intermediate in menaquinone (vitamin K2) biosynthesis. Meganathan R. J Biol Chem, 1981 Sep 25. PMID 7026552
    3. Steady-state kinetics and molecular evolution of Escherichia coli MenD [(1R,6R)-2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase], an anomalous thiamin diphosphate-dependent decarboxylase-carboligase. Bhasin M, et al. Biochemistry, 2003 Nov 25. PMID 14621995
    4. Crystallization and preliminary X-ray analysis of (1R,6R)-2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate (SHCHC) synthase (MenD) from Escherichia coli. Sieminska EA, et al. Acta Crystallogr Sect F Struct Biol Cryst Commun, 2005 May 1. PMID 16511076, Free PMC Article
    5. Vitamin K (menaquinone) biosynthesis in bacteria: purification and probable structure of an intermediate prior to o-succinylbenzoate. Emmons GT, et al. Biochem Biophys Res Commun, 1985 Sep 16. PMID 3902015

    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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    Homology

    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 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 
    involved_in small molecule metabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  

    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
      A0AAN5JJR8
      Conserved Domains (1) summary
      PRK07449
      Location:1 → 556
      PRK07449; 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase; Validated
    Nucleotide Protein
    Heading Accession and Version

    Gene LinkOut

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