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P77243

- PRPD_ECOLI

UniProt

P77243 - PRPD_ECOLI

Protein

2-methylcitrate dehydratase

Gene

prpD

Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 122 (01 Oct 2014)
      Sequence version 3 (23 Jan 2007)
      Previous versions | rss
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    Functioni

    Catalyzes the dehydration of 2-methylcitrate to 2-methyl-cis-aconitate. Also seems to be responsible for the residual aconitase activity of the acnAB-null strain.

    Catalytic activityi

    (2S,3S)-2-hydroxybutane-1,2,3-tricarboxylate = (Z)-but-2-ene-1,2,3-tricarboxylate + H2O.1 Publication

    Cofactori

    Binds 1 2Fe-2S cluster.

    Kineticsi

    1. KM=0.44 mM for (2S,3S)-2-methylcitrate1 Publication

    Pathwayi

    GO - Molecular functioni

    1. 2 iron, 2 sulfur cluster binding Source: UniProtKB-KW
    2. 2-methylcitrate dehydratase activity Source: EcoCyc
    3. metal ion binding Source: UniProtKB-KW

    GO - Biological processi

    1. propionate catabolic process, 2-methylcitrate cycle Source: InterPro
    2. propionate metabolic process, methylcitrate cycle Source: EcoliWiki

    Keywords - Molecular functioni

    Lyase

    Keywords - Ligandi

    2Fe-2S, Iron, Iron-sulfur, Metal-binding

    Enzyme and pathway databases

    BioCyciEcoCyc:G6199-MONOMER.
    ECOL316407:JW0325-MONOMER.
    MetaCyc:G6199-MONOMER.
    BRENDAi4.2.1.79. 2026.
    SABIO-RKP77243.
    UniPathwayiUPA00946.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    2-methylcitrate dehydratase (EC:4.2.1.79)
    Gene namesi
    Name:prpD
    Synonyms:yahT
    Ordered Locus Names:b0334, JW0325
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

    Organism-specific databases

    EcoGeneiEG13603. prpD.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methioninei1 – 11Removed1 Publication
    Chaini2 – 4834822-methylcitrate dehydratasePRO_0000215023Add
    BLAST

    Proteomic databases

    PRIDEiP77243.

    Expressioni

    Gene expression databases

    GenevestigatoriP77243.

    Interactioni

    Subunit structurei

    Monomer.

    Protein-protein interaction databases

    DIPiDIP-10580N.
    IntActiP77243. 4 interactions.
    MINTiMINT-1309441.
    STRINGi511145.b0334.

    Structurei

    Secondary structure

    1
    483
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi14 – 2512
    Helixi31 – 5121
    Helixi55 – 584
    Helixi85 – 9814
    Beta strandi107 – 1093
    Helixi113 – 1164
    Helixi117 – 13317
    Helixi141 – 15818
    Turni159 – 1613
    Helixi165 – 1673
    Helixi172 – 18615
    Helixi191 – 20212
    Helixi210 – 2123
    Helixi220 – 24021
    Turni247 – 2515
    Turni253 – 2553
    Helixi257 – 2615
    Beta strandi273 – 2753
    Helixi276 – 2805
    Beta strandi286 – 2883
    Turni291 – 2933
    Helixi294 – 30916
    Helixi314 – 3163
    Beta strandi317 – 3248
    Helixi326 – 3327
    Helixi341 – 3444
    Helixi348 – 35811
    Helixi363 – 3664
    Helixi368 – 3714
    Helixi374 – 3818
    Beta strandi383 – 3875
    Helixi389 – 3968
    Turni398 – 4003
    Beta strandi405 – 4117
    Beta strandi420 – 4223
    Helixi429 – 4313
    Helixi432 – 45019
    Helixi453 – 46412
    Helixi466 – 4716
    Helixi474 – 4785
    Turni479 – 4813

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1SZQX-ray2.70A/B1-483[»]
    ProteinModelPortaliP77243.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP77243.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the PrpD family.Curated

    Phylogenomic databases

    eggNOGiCOG2079.
    HOGENOMiHOG000159916.
    KOiK01720.
    OMAiTAPQWGF.
    OrthoDBiEOG6RC3K5.
    PhylomeDBiP77243.

    Family and domain databases

    InterProiIPR012705. 2Me_IsoCit_deHydtase_PrpD.
    IPR005656. MmgE_PrpD.
    [Graphical view]
    PANTHERiPTHR16943. PTHR16943. 1 hit.
    PfamiPF03972. MmgE_PrpD. 1 hit.
    [Graphical view]
    SUPFAMiSSF103378. SSF103378. 1 hit.
    TIGRFAMsiTIGR02330. prpD. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    P77243-1 [UniParc]FASTAAdd to Basket

    « Hide

    MSAQINNIRP EFDREIVDIV DYVMNYEISS KVAYDTAHYC LLDTLGCGLE    50
    ALEYPACKKL LGPIVPGTVV PNGVRVPGTQ FQLDPVQAAF NIGAMIRWLD 100
    FNDTWLAAEW GHPSDNLGGI LATADWLSRN AVASGKAPLT MKQVLTAMIK 150
    AHEIQGCIAL ENSFNRVGLD HVLLVKVAST AVVAEMLGLT REEILNAVSL 200
    AWVDGQSLRT YRHAPNTGTR KSWAAGDATS RAVRLALMAK TGEMGYPSAL 250
    TAPVWGFYDV SFKGESFRFQ RPYGSYVMEN VLFKISFPAE FHSQTAVEAA 300
    MTLYEQMQAA GKTAADIEKV TIRTHEACIR IIDKKGPLNN PADRDHCIQY 350
    MVAIPLLFGR LTAADYEDNV AQDKRIDALR EKINCFEDPA FTADYHDPEK 400
    RAIANAITLE FTDGTRFEEV VVEYPIGHAR RRQDGIPKLV DKFKINLARQ 450
    FPTRQQQRIL EVSLDRARLE QMPVNEYLDL YVI 483
    Length:483
    Mass (Da):53,952
    Last modified:January 23, 2007 - v3
    Checksum:i965252C8983E6F64
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U73857 Genomic DNA. Translation: AAB18058.1.
    U00096 Genomic DNA. Translation: AAC73437.1.
    AP009048 Genomic DNA. Translation: BAE76116.1.
    PIRiF64760.
    RefSeqiNP_414868.1. NC_000913.3.
    YP_488628.1. NC_007779.1.

    Genome annotation databases

    EnsemblBacteriaiAAC73437; AAC73437; b0334.
    BAE76116; BAE76116; BAE76116.
    GeneIDi12930816.
    945931.
    KEGGiecj:Y75_p0323.
    eco:b0334.
    PATRICi32115799. VBIEscCol129921_0341.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U73857 Genomic DNA. Translation: AAB18058.1 .
    U00096 Genomic DNA. Translation: AAC73437.1 .
    AP009048 Genomic DNA. Translation: BAE76116.1 .
    PIRi F64760.
    RefSeqi NP_414868.1. NC_000913.3.
    YP_488628.1. NC_007779.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1SZQ X-ray 2.70 A/B 1-483 [» ]
    ProteinModelPortali P77243.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    DIPi DIP-10580N.
    IntActi P77243. 4 interactions.
    MINTi MINT-1309441.
    STRINGi 511145.b0334.

    Proteomic databases

    PRIDEi P77243.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAC73437 ; AAC73437 ; b0334 .
    BAE76116 ; BAE76116 ; BAE76116 .
    GeneIDi 12930816.
    945931.
    KEGGi ecj:Y75_p0323.
    eco:b0334.
    PATRICi 32115799. VBIEscCol129921_0341.

    Organism-specific databases

    EchoBASEi EB3371.
    EcoGenei EG13603. prpD.

    Phylogenomic databases

    eggNOGi COG2079.
    HOGENOMi HOG000159916.
    KOi K01720.
    OMAi TAPQWGF.
    OrthoDBi EOG6RC3K5.
    PhylomeDBi P77243.

    Enzyme and pathway databases

    UniPathwayi UPA00946 .
    BioCyci EcoCyc:G6199-MONOMER.
    ECOL316407:JW0325-MONOMER.
    MetaCyc:G6199-MONOMER.
    BRENDAi 4.2.1.79. 2026.
    SABIO-RK P77243.

    Miscellaneous databases

    EvolutionaryTracei P77243.
    PROi P77243.

    Gene expression databases

    Genevestigatori P77243.

    Family and domain databases

    InterProi IPR012705. 2Me_IsoCit_deHydtase_PrpD.
    IPR005656. MmgE_PrpD.
    [Graphical view ]
    PANTHERi PTHR16943. PTHR16943. 1 hit.
    Pfami PF03972. MmgE_PrpD. 1 hit.
    [Graphical view ]
    SUPFAMi SSF103378. SSF103378. 1 hit.
    TIGRFAMsi TIGR02330. prpD. 1 hit.
    ProtoNeti Search...

    Publicationsi

    1. "Sequence of minutes 4-25 of Escherichia coli."
      Chung E., Allen E., Araujo R., Aparicio A.M., Davis K., Duncan M., Federspiel N., Hyman R., Kalman S., Komp C., Kurdi O., Lew H., Lin D., Namath A., Oefner P., Roberts D., Schramm S., Davis R.W.
      Submitted (JAN-1997) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    3. "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.
    4. "AcnC of Escherichia coli is a 2-methylcitrate dehydratase (PrpD) that can use citrate and isocitrate as substrates."
      Blank L., Green J., Guest J.R.
      Microbiology 148:133-146(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 2-13, CHARACTERIZATION.
    5. "Oxidation of propionate to pyruvate in Escherichia coli. Involvement of methylcitrate dehydratase and aconitase."
      Brock M., Maerker C., Schuetz A., Voelker U., Buckel W.
      Eur. J. Biochem. 269:6184-6194(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, BIOPHYSICOCHEMICAL PROPERTIES.
    6. "Crystal structure of 2-methylcitrate dehydratase."
      New York structural genomix research consortium (NYSGXRC)
      Submitted (FEB-2009) to the PDB data bank
      Cited for: X-RAY CRYSTALLOGRAPHY (2.7 ANGSTROMS).

    Entry informationi

    Entry nameiPRPD_ECOLI
    AccessioniPrimary (citable) accession number: P77243
    Secondary accession number(s): Q2MC90
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 1, 1997
    Last sequence update: January 23, 2007
    Last modified: October 1, 2014
    This is version 122 of the entry and version 3 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Direct protein sequencing, 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