Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Basket 0
(max 400 entries)x

Your basket is currently empty.

Select item(s) and click on "Add to basket" to create your own collection here
(400 entries max)

P17109

- MEND_ECOLI

UniProt

P17109 - MEND_ECOLI

Protein

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

Gene

menD

Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
    • BLAST
    • Align
    • Format
    • Add to basket
    • History
      Entry version 132 (01 Oct 2014)
      Sequence version 4 (01 Nov 1997)
      Previous versions | rss
    • Help video
    • Feedback
    • Comment

    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).1 Publication

    Catalytic activityi

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

    Cofactori

    Magnesium or manganese.
    Binds 1 thiamine pyrophosphate per subunit.

    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

    GO - Molecular functioni

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

    GO - Biological processi

    1. menaquinone biosynthetic process Source: EcoCyc

    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.
    SABIO-RKP17109.
    UniPathwayiUPA00079; UER00164.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase (EC:2.2.1.9)
    Short name:
    SEPHCHC synthase
    Alternative name(s):
    Menaquinone biosynthesis protein MenD
    Gene namesi
    Name:menD
    Ordered Locus Names:b2264, JW5374
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

    Organism-specific databases

    EcoGeneiEG10579. menD.

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi55 – 551E → Q: Loss of activity. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 5565562-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthasePRO_0000090829Add
    BLAST

    Proteomic databases

    PaxDbiP17109.
    PRIDEiP17109.

    Expressioni

    Inductioni

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

    Gene expression databases

    GenevestigatoriP17109.

    Interactioni

    Subunit structurei

    Homodimer.2 Publications

    Protein-protein interaction databases

    DIPiDIP-10185N.
    IntActiP17109. 1 interaction.
    MINTiMINT-1246688.
    STRINGi511145.b2264.

    Structurei

    Secondary structure

    1
    556
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi3 – 1917
    Turni20 – 223
    Beta strandi25 – 284
    Turni32 – 343
    Helixi35 – 439
    Beta strandi48 – 514
    Helixi55 – 6915
    Beta strandi73 – 775
    Helixi81 – 844
    Helixi87 – 9610
    Beta strandi100 – 1067
    Helixi109 – 1113
    Beta strandi112 – 1154
    Turni123 – 1286
    Beta strandi130 – 1356
    Helixi145 – 15713
    Beta strandi164 – 1696
    Helixi183 – 1875
    Helixi188 – 1947
    Beta strandi199 – 2013
    Beta strandi205 – 2073
    Helixi214 – 2174
    Beta strandi222 – 2265
    Helixi231 – 24414
    Beta strandi248 – 2503
    Turni252 – 2543
    Helixi263 – 2664
    Helixi270 – 2767
    Beta strandi280 – 2878
    Helixi292 – 3009
    Beta strandi304 – 3129
    Beta strandi322 – 3287
    Helixi330 – 3367
    Helixi349 – 36113
    Turni362 – 3654
    Beta strandi366 – 3683
    Helixi369 – 3746
    Helixi376 – 3783
    Beta strandi385 – 3884
    Helixi392 – 4009
    Beta strandi409 – 4113
    Beta strandi418 – 4203
    Helixi421 – 43212
    Beta strandi436 – 4416
    Helixi442 – 4476
    Helixi449 – 4513
    Helixi452 – 4554
    Beta strandi462 – 4698
    Helixi474 – 4774
    Helixi482 – 4887
    Helixi498 – 5036
    Beta strandi507 – 5093
    Helixi514 – 52411
    Beta strandi527 – 53610
    Helixi541 – 55414

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    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[»]
    ProteinModelPortaliP17109.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP17109.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the TPP enzyme family. MenD subfamily.Curated

    Phylogenomic databases

    eggNOGiCOG1165.
    HOGENOMiHOG000218360.
    KOiK02551.
    OMAiQKPWLLE.
    OrthoDBiEOG6NWBQW.
    PhylomeDBiP17109.

    Family and domain databases

    Gene3Di3.40.50.970. 2 hits.
    HAMAPiMF_01659. MenD.
    InterProiIPR004433. MenaQ_synth_MenD.
    IPR029061. THDP-binding.
    IPR012001. Thiamin_PyroP_enz_TPP-bd_dom.
    IPR011766. TPP_enzyme-bd_C.
    [Graphical view]
    PfamiPF02775. TPP_enzyme_C. 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

    MSVSAFNRRW AAVILEALTR HGVRHICIAP GSRSTPLTLA AAENSAFIHH    50
    THFDERGLGH LALGLAKVSK QPVAVIVTSG TAVANLYPAL IEAGLTGEKL 100
    ILLTADRPPE LIDCGANQAI RQPGMFASHP THSISLPRPT QDIPARWLVS 150
    TIDHALGTLH AGGVHINCPF AEPLYGEMDD TGLSWQQRLG DWWQDDKPWL 200
    REAPRLESEK QRDWFFWRQK RGVVVAGRMS AEEGKKVALW AQTLGWPLIG 250
    DVLSQTGQPL PCADLWLGNA KATSELQQAQ IVVQLGSSLT GKRLLQWQAS 300
    CEPEEYWIVD DIEGRLDPAH HRGRRLIANI ADWLELHPAE KRQPWCVEIP 350
    RLAEQAMQAV IARRDAFGEA QLAHRICDYL PEQGQLFVGN SLVVRLIDAL 400
    SQLPAGYPVY SNRGASGIDG LLSTAAGVQR ASGKPTLAIV GDLSALYDLN 450
    ALALLRQVSA PLVLIVVNNN GGQIFSLLPT PQSERERFYL MPQNVHFEHA 500
    AAMFELKYHR PQNWQELETA FADAWRTPTT TVIEMVVNDT DGAQTLQQLL 550
    AQVSHL 556
    Length:556
    Mass (Da):61,367
    Last modified:November 1, 1997 - v4
    Checksum:i278201D02243E76D
    GO

    Sequence cautioni

    The sequence AAA24153.1 differs from that shown. Reason: Frameshift at position 370.

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti42 – 421Missing in AAA24153. (PubMed:2666397)Curated
    Sequence conflicti163 – 18321GVHIN…DDTGL → ESISTARLLNRCMAKWTIPG F in AAA24153. (PubMed:2666397)CuratedAdd
    BLAST
    Sequence conflicti398 – 3981Missing in AAA24153. (PubMed:2666397)Curated
    Sequence conflicti543 – 55614AQTLQ…QVSHL → RKRSSNFWRR in AAB59060. 1 PublicationCuratedAdd
    BLAST

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    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.
    YP_490504.1. NC_007779.1.

    Genome annotation databases

    EnsemblBacteriaiAAC75324; AAC75324; b2264.
    BAA16089; BAA16089; BAA16089.
    GeneIDi12931512.
    946720.
    KEGGiecj:Y75_p2228.
    eco:b2264.
    PATRICi32119895. VBIEscCol129921_2357.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    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 .
    PIRi F64997.
    RefSeqi NP_416767.1. NC_000913.3.
    YP_490504.1. NC_007779.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    2JLA X-ray 2.81 A/B/C/D 1-556 [» ]
    2JLC X-ray 2.50 A/B 1-556 [» ]
    3FLM X-ray 2.70 A/B 1-556 [» ]
    3HWW X-ray 1.95 A/D 1-556 [» ]
    3HWX X-ray 2.60 1/A/B/I/J/R/S/Z 1-556 [» ]
    ProteinModelPortali P17109.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    DIPi DIP-10185N.
    IntActi P17109. 1 interaction.
    MINTi MINT-1246688.
    STRINGi 511145.b2264.

    Proteomic databases

    PaxDbi P17109.
    PRIDEi P17109.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAC75324 ; AAC75324 ; b2264 .
    BAA16089 ; BAA16089 ; BAA16089 .
    GeneIDi 12931512.
    946720.
    KEGGi ecj:Y75_p2228.
    eco:b2264.
    PATRICi 32119895. VBIEscCol129921_2357.

    Organism-specific databases

    EchoBASEi EB0574.
    EcoGenei EG10579. menD.

    Phylogenomic databases

    eggNOGi COG1165.
    HOGENOMi HOG000218360.
    KOi K02551.
    OMAi QKPWLLE.
    OrthoDBi EOG6NWBQW.
    PhylomeDBi P17109.

    Enzyme and pathway databases

    UniPathwayi UPA00079 ; UER00164 .
    BioCyci EcoCyc:MEND-MONOMER.
    ECOL316407:JW5374-MONOMER.
    MetaCyc:MEND-MONOMER.
    SABIO-RK P17109.

    Miscellaneous databases

    EvolutionaryTracei P17109.
    PROi P17109.

    Gene expression databases

    Genevestigatori P17109.

    Family and domain databases

    Gene3Di 3.40.50.970. 2 hits.
    HAMAPi MF_01659. MenD.
    InterProi IPR004433. MenaQ_synth_MenD.
    IPR029061. THDP-binding.
    IPR012001. Thiamin_PyroP_enz_TPP-bd_dom.
    IPR011766. TPP_enzyme-bd_C.
    [Graphical view ]
    Pfami PF02775. TPP_enzyme_C. 1 hit.
    PF02776. TPP_enzyme_N. 1 hit.
    [Graphical view ]
    PIRSFi PIRSF004983. MenD. 1 hit.
    SUPFAMi SSF52518. SSF52518. 2 hits.
    TIGRFAMsi TIGR00173. menD. 1 hit.
    ProtoNeti Search...

    Publicationsi

    1. "A new isochorismate synthase specifically involved in menaquinone (vitamin K2) biosynthesis encoded by the menF gene."
      Daruwala R., Kwon O., Meganathan R., Hudspeth M.E.S.
      FEMS Microbiol. Lett. 140:159-163(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    2. "Construction of a contiguous 874-kb sequence of the Escherichia coli-K12 genome corresponding to 50.0-68.8 min on the linkage map and analysis of its sequence features."
      Yamamoto Y., Aiba H., Baba T., Hayashi K., Inada T., Isono K., Itoh T., Kimura S., Kitagawa M., Makino K., Miki T., Mitsuhashi N., Mizobuchi K., Mori H., Nakade S., Nakamura Y., Nashimoto H., Oshima T.
      , Oyama S., Saito N., Sampei G., Satoh Y., Sivasundaram S., Tagami H., Takahashi H., Takeda J., Takemoto K., Uehara K., Wada C., Yamagata S., Horiuchi T.
      DNA Res. 4:91-113(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    4. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
      Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
      Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    5. "Sequence and overexpression of the menD gene from Escherichia coli."
      Popp J.L.
      J. Bacteriol. 171:4349-4354(1989) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-507.
    6. Sharma V., Hudspeth M.E., Meganathan R.
      Submitted (JUL-1994) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 536-556.
      Strain: K12.
    7. "Menaquinone (vitamin K2) biosynthesis: evidence that the Escherichia coli menD gene encodes both 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylic acid synthase and alpha-ketoglutarate decarboxylase activities."
      Palaniappan C., Sharma V., Hudspeth M.E., Meganathan R.
      J. Bacteriol. 174:8111-8118(1992) [PubMed] [Europe PMC] [Abstract]
      Cited for: INDUCTION, PRELIMINARY FUNCTION.
      Strain: K12.
    8. "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., Billinsky J.L., Palmer D.R.J.
      Biochemistry 42:13496-13504(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: SUBUNIT, COFACTOR, MUTAGENESIS OF GLU-55, BIOPHYSICOCHEMICAL PROPERTIES.
    9. "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 E.A.L., Macova A., Palmer D.R.J., Sanders D.A.R.
      Acta Crystallogr. F 61:489-492(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: CRYSTALLIZATION, COFACTOR, SUBUNIT.
    10. "Menaquinone biosynthesis in Escherichia coli: identification of 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate as a novel intermediate and re-evaluation of MenD activity."
      Jiang M., Cao Y., Guo Z.-F., Chen M., Chen X., Guo Z.
      Biochemistry 46:10979-10989(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION AS A SEPHCHC SYNTHASE, CATALYTIC ACTIVITY, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES.

    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: October 1, 2014
    This is version 132 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

    External Data

    Dasty 3