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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: -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

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

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

    • 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase activity Source: EcoCyc
    • metal ion binding Source: UniProtKB-KW
    • thiamine pyrophosphate binding Source: EcoCyc

    GO - Biological processi

    • menaquinone biosynthetic process Source: EcoCyc

    Keywordsi

    Molecular functionTransferase
    Biological processMenaquinone biosynthesis
    LigandMagnesium, Manganese, Metal-binding, Thiamine pyrophosphate

    Enzyme and pathway databases

    BioCyciEcoCyc:MEND-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, 9 interactors
    DIPiDIP-10185N
    IntActiP17109, 1 interactor
    STRINGi316385.ECDH10B_2425

    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[»]
    5EJMX-ray1.72A/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

    HAMAPiMF_01659 MenD, 1 hit
    InterProiView protein in InterPro
    IPR004433 MenaQ_synth_MenD
    IPR032264 MenD_middle
    IPR029061 THDP-binding
    IPR012001 Thiamin_PyroP_enz_TPP-bd_dom
    IPR011766 TPP_enzyme-bd_C
    PANTHERiPTHR42916 PTHR42916, 1 hit
    PfamiView protein in Pfam
    PF02775 TPP_enzyme_C, 1 hit
    PF16582 TPP_enzyme_M_2, 1 hit
    PF02776 TPP_enzyme_N, 1 hit
    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
    PATRICifig|511145.12.peg.2357

    Similar proteinsi

    Entry informationi

    Entry nameiMEND_ECOLI
    AccessioniPrimary (citable) accession number: P17109
    Secondary accession number(s): P76478, P78180, P78181
    Entry historyiIntegrated into UniProtKB/Swiss-Prot: August 1, 1990
    Last sequence update: November 1, 1997
    Last modified: March 28, 2018
    This is version 154 of the entry and version 4 of the sequence. See complete history.
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

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