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Protein

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

Gene

menD

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

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 annotation1 Publication

Catalytic activityi

Isochorismate + 2-oxoglutarate = 5-enolpyruvoyl-6-hydroxy-2-succinyl-cyclohex-3-ene-1-carboxylate + CO2.UniRule annotation1 Publication

Cofactori

Protein has several cofactor binding sites:
  • Mg2+UniRule annotation, Mn2+UniRule annotation
  • thiamine diphosphateUniRule annotationNote: Binds 1 thiamine pyrophosphate per subunit.UniRule annotation

Kineticsi

  1. KM=53 nM for isochorismate (at 22.5 degrees Celsius and pH 7.8)2 Publications
  2. KM=1.5 µM for 2-oxoglutarate (at 22.5 degrees Celsius and pH 7.8)2 Publications
  3. KM=2.4 µM for thiamine diphosphate (at 22.5 degrees Celsius and pH 7.8)2 Publications
  4. KM=80 µM for magnesium ions (at 22.5 degrees Celsius and pH 7.8)2 Publications

    pH dependencei

    Optimum pH is 7-8.2 Publications

    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. Isochorismate synthase MenF (menF)
    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. 2-succinylbenzoate--CoA ligase (menE)
    6. 1,4-dihydroxy-2-naphthoyl-CoA synthase (menB)
    7. 1,4-dihydroxy-2-naphthoyl-CoA hydrolase (menI)
    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

    • menaquinone biosynthetic process Source: EcoCyc
    Complete GO annotation...

    Keywords - Molecular functioni

    Transferase

    Keywords - Biological processi

    Menaquinone biosynthesis

    Keywords - Ligandi

    Magnesium, Manganese, Metal-binding, Thiamine pyrophosphate

    Enzyme and pathway databases

    BioCyciEcoCyc:MEND-MONOMER.
    ECOL316407:JW5374-MONOMER.
    MetaCyc:MEND-MONOMER.
    BRENDAi2.2.1.9. 2165.
    SABIO-RKP17109.
    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:b2264, JW5374
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG10579. menD.

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi55E → Q: Loss of activity. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00000908291 – 5562-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthaseAdd BLAST556

    Proteomic databases

    PaxDbiP17109.
    PRIDEiP17109.

    Expressioni

    Inductioni

    By isopropyl-beta-D-thiogalactoside (IPTG).1 Publication

    Interactioni

    Subunit structurei

    Homodimer.UniRule annotation2 Publications

    Protein-protein interaction databases

    BioGridi4260506. 8 interactors.
    DIPiDIP-10185N.
    IntActiP17109. 1 interactor.
    MINTiMINT-1246688.
    STRINGi511145.b2264.

    Structurei

    Secondary structure

    1556
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Helixi3 – 19Combined sources17
    Turni20 – 22Combined sources3
    Beta strandi25 – 28Combined sources4
    Turni32 – 34Combined sources3
    Helixi35 – 43Combined sources9
    Beta strandi48 – 51Combined sources4
    Helixi55 – 69Combined sources15
    Beta strandi73 – 77Combined sources5
    Helixi81 – 84Combined sources4
    Helixi87 – 96Combined sources10
    Beta strandi100 – 106Combined sources7
    Helixi109 – 111Combined sources3
    Beta strandi112 – 114Combined sources3
    Turni123 – 128Combined sources6
    Beta strandi130 – 135Combined sources6
    Helixi145 – 157Combined sources13
    Beta strandi164 – 169Combined sources6
    Helixi183 – 187Combined sources5
    Helixi188 – 194Combined sources7
    Beta strandi199 – 201Combined sources3
    Beta strandi205 – 207Combined sources3
    Helixi214 – 217Combined sources4
    Beta strandi222 – 226Combined sources5
    Helixi231 – 244Combined sources14
    Beta strandi248 – 250Combined sources3
    Turni252 – 254Combined sources3
    Helixi263 – 266Combined sources4
    Helixi270 – 276Combined sources7
    Beta strandi280 – 287Combined sources8
    Helixi292 – 300Combined sources9
    Beta strandi304 – 312Combined sources9
    Beta strandi322 – 328Combined sources7
    Helixi330 – 336Combined sources7
    Helixi349 – 361Combined sources13
    Turni362 – 365Combined sources4
    Beta strandi366 – 368Combined sources3
    Helixi369 – 374Combined sources6
    Helixi376 – 379Combined sources4
    Beta strandi385 – 388Combined sources4
    Helixi392 – 400Combined sources9
    Beta strandi409 – 411Combined sources3
    Beta strandi418 – 420Combined sources3
    Helixi421 – 432Combined sources12
    Beta strandi436 – 441Combined sources6
    Helixi442 – 447Combined sources6
    Helixi449 – 456Combined sources8
    Beta strandi462 – 468Combined sources7
    Helixi474 – 477Combined sources4
    Helixi482 – 488Combined sources7
    Helixi498 – 503Combined sources6
    Beta strandi507 – 509Combined sources3
    Helixi514 – 524Combined sources11
    Beta strandi527 – 536Combined sources10
    Helixi541 – 554Combined sources14

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    2JLAX-ray2.81A/B/C/D1-556[»]
    2JLCX-ray2.50A/B1-556[»]
    3FLMX-ray2.70A/B1-556[»]
    3HWWX-ray1.95A/D1-556[»]
    3HWXX-ray2.601/A/B/I/J/R/S/Z1-556[»]
    5EJ4X-ray1.77A/B/C/D/E/F/G/H1-556[»]
    5EJ5X-ray2.30A/B/C/D/E/F/G/H1-556[»]
    5EJ6X-ray2.24A/B/C/D/E/F/G/H1-556[»]
    5EJ7X-ray1.56A/B/C/D/E/F/G/H1-556[»]
    5EJ8X-ray1.34A/B/C/D/E/F/G/H1-556[»]
    5EJ9X-ray1.72A/B/C/D/E/F/G/H1-556[»]
    5EJAX-ray1.60A/B/C/D/E/F/G/H1-556[»]
    ProteinModelPortaliP17109.
    SMRiP17109.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP17109.

    Family & Domainsi

    Sequence similaritiesi

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

    Phylogenomic databases

    eggNOGiENOG4105C4A. Bacteria.
    COG1165. LUCA.
    HOGENOMiHOG000218360.
    InParanoidiP17109.
    KOiK02551.
    OMAiIFRILPG.
    PhylomeDBiP17109.

    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.

    P17109-1 [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:November 1, 1997 - v4
    Checksum:i278201D02243E76D
    GO

    Sequence cautioni

    The sequence AAA24153 differs from that shown. Reason: Frameshift at position 370.Curated

    Experimental Info

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Sequence conflicti42Missing in AAA24153 (PubMed:2666397).Curated1
    Sequence conflicti163 – 183GVHIN…DDTGL → ESISTARLLNRCMAKWTIPG F in AAA24153 (PubMed:2666397).CuratedAdd BLAST21
    Sequence conflicti398Missing in AAA24153 (PubMed:2666397).Curated1
    Sequence conflicti543 – 556AQTLQ…QVSHL → RKRSSNFWRR in AAB59060 (Ref. 6) CuratedAdd BLAST14

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U54790 Genomic DNA. Translation: AAC44304.1.
    U00096 Genomic DNA. Translation: AAC75324.1.
    AP009048 Genomic DNA. Translation: BAA16089.2.
    M21787 Genomic DNA. Translation: AAA24153.1. Frameshift.
    L04464 Genomic DNA. Translation: AAB59060.1.
    L35030 Genomic DNA. Translation: AAA24150.1.
    PIRiF64997.
    RefSeqiNP_416767.1. NC_000913.3.
    WP_001295284.1. NZ_LN832404.1.

    Genome annotation databases

    EnsemblBacteriaiAAC75324; AAC75324; b2264.
    BAA16089; BAA16089; BAA16089.
    GeneIDi946720.
    KEGGiecj:JW5374.
    eco:b2264.
    PATRICi32119895. VBIEscCol129921_2357.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U54790 Genomic DNA. Translation: AAC44304.1.
    U00096 Genomic DNA. Translation: AAC75324.1.
    AP009048 Genomic DNA. Translation: BAA16089.2.
    M21787 Genomic DNA. Translation: AAA24153.1. Frameshift.
    L04464 Genomic DNA. Translation: AAB59060.1.
    L35030 Genomic DNA. Translation: AAA24150.1.
    PIRiF64997.
    RefSeqiNP_416767.1. NC_000913.3.
    WP_001295284.1. NZ_LN832404.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    2JLAX-ray2.81A/B/C/D1-556[»]
    2JLCX-ray2.50A/B1-556[»]
    3FLMX-ray2.70A/B1-556[»]
    3HWWX-ray1.95A/D1-556[»]
    3HWXX-ray2.601/A/B/I/J/R/S/Z1-556[»]
    5EJ4X-ray1.77A/B/C/D/E/F/G/H1-556[»]
    5EJ5X-ray2.30A/B/C/D/E/F/G/H1-556[»]
    5EJ6X-ray2.24A/B/C/D/E/F/G/H1-556[»]
    5EJ7X-ray1.56A/B/C/D/E/F/G/H1-556[»]
    5EJ8X-ray1.34A/B/C/D/E/F/G/H1-556[»]
    5EJ9X-ray1.72A/B/C/D/E/F/G/H1-556[»]
    5EJAX-ray1.60A/B/C/D/E/F/G/H1-556[»]
    ProteinModelPortaliP17109.
    SMRiP17109.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi4260506. 8 interactors.
    DIPiDIP-10185N.
    IntActiP17109. 1 interactor.
    MINTiMINT-1246688.
    STRINGi511145.b2264.

    Proteomic databases

    PaxDbiP17109.
    PRIDEiP17109.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC75324; AAC75324; b2264.
    BAA16089; BAA16089; BAA16089.
    GeneIDi946720.
    KEGGiecj:JW5374.
    eco:b2264.
    PATRICi32119895. VBIEscCol129921_2357.

    Organism-specific databases

    EchoBASEiEB0574.
    EcoGeneiEG10579. menD.

    Phylogenomic databases

    eggNOGiENOG4105C4A. Bacteria.
    COG1165. LUCA.
    HOGENOMiHOG000218360.
    InParanoidiP17109.
    KOiK02551.
    OMAiIFRILPG.
    PhylomeDBiP17109.

    Enzyme and pathway databases

    UniPathwayiUPA00079.
    UPA01057; UER00164.
    BioCyciEcoCyc:MEND-MONOMER.
    ECOL316407:JW5374-MONOMER.
    MetaCyc:MEND-MONOMER.
    BRENDAi2.2.1.9. 2165.
    SABIO-RKP17109.

    Miscellaneous databases

    EvolutionaryTraceiP17109.
    PROiP17109.

    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_ECOLI
    AccessioniPrimary (citable) accession number: P17109
    Secondary accession number(s): P76478, P78180, P78181
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: August 1, 1990
    Last sequence update: November 1, 1997
    Last modified: November 2, 2016
    This is version 146 of the entry and version 4 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Caution

    Was originally thought (PubMed:1459959, PubMed:14621995 and PubMed:16511076) to be a 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate (SHCHC) synthase but further protein analysis clearly suggests that it is a 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate (SEPHCHC) synthase.1 Publication

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. Escherichia coli
      Escherichia coli (strain K12): entries and cross-references to EcoGene
    2. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    3. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    4. 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.