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Protein

2-methylcitrate dehydratase

Gene

prpD

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

Functioni

Involved in the catabolism of short chain fatty acids (SCFA) via the tricarboxylic acid (TCA)(acetyl degradation route) and via the 2-methylcitrate cycle I (propionate degradation route). Catalyzes the stereospecific dehydration of (2S,3S)-2-methylcitrate (2-MC) to yield the cis isomer of 2-methyl-aconitate. It is also able to catalyze the dehydration of citrate and the hydration of cis-aconitate at a lower rate. Due to its broad substrate specificity, it seems to be responsible for the residual aconitase activity of the acnAB-null mutant.2 Publications

Catalytic activityi

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

Kineticsi

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

    Pathway: propanoate degradation

    This protein is involved in the pathway propanoate degradation, which is part of Organic acid metabolism.1 Publication
    View all proteins of this organism that are known to be involved in the pathway propanoate degradation and in Organic acid metabolism.

    Pathway: tricarboxylic acid cycle

    This protein is involved in step 2 of the subpathway that synthesizes isocitrate from oxaloacetate.1 Publication
    Proteins known to be involved in the 2 steps of the subpathway in this organism are:
    1. Citrate synthase (gltA), Citrate synthase (gltA)
    2. Aconitate hydratase B (acnB), 2-methylcitrate dehydratase (prpD), Aconitate hydratase B (acnB), Aconitate hydratase A (acnA), 2-methylcitrate synthase (prpC)
    This subpathway is part of the pathway tricarboxylic acid cycle, which is itself part of Carbohydrate metabolism.
    View all proteins of this organism that are known to be involved in the subpathway that synthesizes isocitrate from oxaloacetate, the pathway tricarboxylic acid cycle and in Carbohydrate metabolism.

    GO - Molecular functioni

    • 2 iron, 2 sulfur cluster binding Source: UniProtKB
    • 2-methylcitrate dehydratase activity Source: EcoCyc
    • aconitate hydratase activity Source: UniProtKB-EC

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Lyase

    Keywords - Biological processi

    Tricarboxylic acid cycle

    Enzyme and pathway databases

    BioCyciEcoCyc:G6199-MONOMER.
    ECOL316407:JW0325-MONOMER.
    MetaCyc:G6199-MONOMER.
    BRENDAi4.2.1.79. 2026.
    SABIO-RKP77243.
    UniPathwayiUPA00223; UER00718.
    UPA00946.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    2-methylcitrate dehydratase1 Publication (EC:4.2.1.792 Publications)
    Short name:
    2-MC dehydratase1 Publication
    Alternative name(s):
    (2S,3S)-2-methylcitrate dehydratase1 Publication
    Aconitate hydratase1 Publication (EC:4.2.1.32 Publications)
    Short name:
    ACN1 Publication
    Short name:
    Aconitase1 Publication
    Gene namesi
    Name:prpD1 Publication
    Synonyms:yahT
    Ordered Locus Names:b0334, JW0325
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    ProteomesiUP000000318 Componenti: Chromosome UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG13603. prpD.

    Pathology & Biotechi

    Disruption phenotypei

    Cells lacking this gene abolished the residual aconitase activity of an AcnAB-null strain.1 Publication

    PTM / Processingi

    Molecule processing

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

    Proteomic databases

    PRIDEiP77243.

    Expressioni

    Inductioni

    By propionate, but not acetate or glucose. Expression of prpBCDE operon is regulated by PrpR, CRP and a variety of sugars such as arabinose, galactose, glucose mannose and xylose.3 Publications

    Interactioni

    Subunit structurei

    Monomer.2 Publications

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

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1SZQX-ray2.70A/B1-483[»]
    ProteinModelPortaliP77243.
    SMRiP77243. Positions 11-483.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP77243.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the PrpD family.Curated

    Phylogenomic databases

    eggNOGiCOG2079.
    HOGENOMiHOG000159916.
    InParanoidiP77243.
    KOiK01720.
    OMAiCLMDTLG.
    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

            10         20         30         40         50
    MSAQINNIRP EFDREIVDIV DYVMNYEISS KVAYDTAHYC LLDTLGCGLE
    60 70 80 90 100
    ALEYPACKKL LGPIVPGTVV PNGVRVPGTQ FQLDPVQAAF NIGAMIRWLD
    110 120 130 140 150
    FNDTWLAAEW GHPSDNLGGI LATADWLSRN AVASGKAPLT MKQVLTAMIK
    160 170 180 190 200
    AHEIQGCIAL ENSFNRVGLD HVLLVKVAST AVVAEMLGLT REEILNAVSL
    210 220 230 240 250
    AWVDGQSLRT YRHAPNTGTR KSWAAGDATS RAVRLALMAK TGEMGYPSAL
    260 270 280 290 300
    TAPVWGFYDV SFKGESFRFQ RPYGSYVMEN VLFKISFPAE FHSQTAVEAA
    310 320 330 340 350
    MTLYEQMQAA GKTAADIEKV TIRTHEACIR IIDKKGPLNN PADRDHCIQY
    360 370 380 390 400
    MVAIPLLFGR LTAADYEDNV AQDKRIDALR EKINCFEDPA FTADYHDPEK
    410 420 430 440 450
    RAIANAITLE FTDGTRFEEV VVEYPIGHAR RRQDGIPKLV DKFKINLARQ
    460 470 480
    FPTRQQQRIL EVSLDRARLE QMPVNEYLDL YVI
    Length:483
    Mass (Da):53,952
    Last modified:January 23, 2007 - v3
    Checksum:i965252C8983E6F64
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    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.

    Genome annotation databases

    EnsemblBacteriaiAAC73437; AAC73437; b0334.
    BAE76116; BAE76116; BAE76116.
    GeneIDi945931.
    KEGGiecj:Y75_p0323.
    eco:b0334.
    PATRICi32115799. VBIEscCol129921_0341.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    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.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1SZQX-ray2.70A/B1-483[»]
    ProteinModelPortaliP77243.
    SMRiP77243. Positions 11-483.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

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

    Proteomic databases

    PRIDEiP77243.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC73437; AAC73437; b0334.
    BAE76116; BAE76116; BAE76116.
    GeneIDi945931.
    KEGGiecj:Y75_p0323.
    eco:b0334.
    PATRICi32115799. VBIEscCol129921_0341.

    Organism-specific databases

    EchoBASEiEB3371.
    EcoGeneiEG13603. prpD.

    Phylogenomic databases

    eggNOGiCOG2079.
    HOGENOMiHOG000159916.
    InParanoidiP77243.
    KOiK01720.
    OMAiCLMDTLG.
    OrthoDBiEOG6RC3K5.
    PhylomeDBiP77243.

    Enzyme and pathway databases

    UniPathwayiUPA00223; UER00718.
    UPA00946.
    BioCyciEcoCyc:G6199-MONOMER.
    ECOL316407:JW0325-MONOMER.
    MetaCyc:G6199-MONOMER.
    BRENDAi4.2.1.79. 2026.
    SABIO-RKP77243.

    Miscellaneous databases

    EvolutionaryTraceiP77243.
    PROiP77243.

    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.
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    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, FUNCTION, CATALYTIC ACTIVITY, DISRUPTION PHENOTYPE, SUBSTRATE SPECIFICITY, SUBUNIT.
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    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: FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, INDUCTION, SUBSTRATE SPECIFICITY, REACTION MECHANISM.
      Strain: K12.
    6. "Catabolite repression of the propionate catabolic genes in Escherichia coli and Salmonella enterica: evidence for involvement of the cyclic AMP receptor protein."
      Lee S.K., Newman J.D., Keasling J.D.
      J. Bacteriol. 187:2793-2800(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: INDUCTION.
      Strain: K12.
    7. "The mechanism of sugar-mediated catabolite repression of the propionate catabolic genes in Escherichia coli."
      Park J.M., Vinuselvi P., Lee S.K.
      Gene 504:116-121(2012) [PubMed] [Europe PMC] [Abstract]
      Cited for: INDUCTION.
      Strain: K12.
    8. "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), SUBUNIT.
      Strain: K12.

    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: June 24, 2015
    This is version 129 of the entry and version 3 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    PrpD catalyzes an unusual syn elimination, whereas the addition of water by AcnB to cis-2-methylaconitate occurs in the usual anti manner.1 Publication

    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

    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 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.