PRPD_ECOLI
ID PRPD_ECOLI Reviewed; 483 AA.
AC P77243; Q2MC90;
DT 01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 3.
DT 03-AUG-2022, entry version 166.
DE RecName: Full=2-methylcitrate dehydratase {ECO:0000303|PubMed:11782506};
DE Short=2-MC dehydratase {ECO:0000303|PubMed:12473114};
DE EC=4.2.1.79 {ECO:0000269|PubMed:11782506, ECO:0000269|PubMed:12473114};
DE AltName: Full=(2S,3S)-2-methylcitrate dehydratase {ECO:0000305|PubMed:12473114};
DE AltName: Full=Aconitate hydratase {ECO:0000303|PubMed:11782506};
DE Short=ACN {ECO:0000303|PubMed:11782506};
DE Short=Aconitase {ECO:0000303|PubMed:11782506};
DE EC=4.2.1.3 {ECO:0000269|PubMed:11782506, ECO:0000269|PubMed:12473114};
GN Name=prpD {ECO:0000303|PubMed:11782506}; Synonyms=yahT;
GN OrderedLocusNames=b0334, JW0325;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RA Chung E., Allen E., Araujo R., Aparicio A.M., Davis K., Duncan M.,
RA Federspiel N., Hyman R., Kalman S., Komp C., Kurdi O., Lew H., Lin D.,
RA Namath A., Oefner P., Roberts D., Schramm S., Davis R.W.;
RT "Sequence of minutes 4-25 of Escherichia coli.";
RL Submitted (JAN-1997) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [4]
RP PROTEIN SEQUENCE OF 2-13, FUNCTION, CATALYTIC ACTIVITY, DISRUPTION
RP PHENOTYPE, SUBSTRATE SPECIFICITY, AND SUBUNIT.
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=11782506; DOI=10.1099/00221287-148-1-133;
RA Blank L., Green J., Guest J.R.;
RT "AcnC of Escherichia coli is a 2-methylcitrate dehydratase (PrpD) that can
RT use citrate and isocitrate as substrates.";
RL Microbiology 148:133-146(2002).
RN [5]
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, INDUCTION,
RP SUBSTRATE SPECIFICITY, AND REACTION MECHANISM.
RC STRAIN=K12;
RX PubMed=12473114; DOI=10.1046/j.1432-1033.2002.03336.x;
RA Brock M., Maerker C., Schuetz A., Voelker U., Buckel W.;
RT "Oxidation of propionate to pyruvate in Escherichia coli. Involvement of
RT methylcitrate dehydratase and aconitase.";
RL Eur. J. Biochem. 269:6184-6194(2002).
RN [6]
RP INDUCTION.
RC STRAIN=K12;
RX PubMed=15805526; DOI=10.1128/jb.187.8.2793-2800.2005;
RA Lee S.K., Newman J.D., Keasling J.D.;
RT "Catabolite repression of the propionate catabolic genes in Escherichia
RT coli and Salmonella enterica: evidence for involvement of the cyclic AMP
RT receptor protein.";
RL J. Bacteriol. 187:2793-2800(2005).
RN [7]
RP INDUCTION.
RC STRAIN=K12;
RX PubMed=22579471; DOI=10.1016/j.gene.2012.04.074;
RA Park J.M., Vinuselvi P., Lee S.K.;
RT "The mechanism of sugar-mediated catabolite repression of the propionate
RT catabolic genes in Escherichia coli.";
RL Gene 504:116-121(2012).
RN [8]
RP FUNCTION, AND DISCUSSION OF STEREOCHEMISTRY.
RX PubMed=28956599; DOI=10.1021/acs.biochem.7b00778;
RA Reddick J.J., Sirkisoon S., Dahal R.A., Hardesty G., Hage N.E., Booth W.T.,
RA Quattlebaum A.L., Mills S.N., Meadows V.G., Adams S.L.H., Doyle J.S.,
RA Kiel B.E.;
RT "First biochemical characterization of a methylcitric acid cycle from
RT Bacillus subtilis strain 168.";
RL Biochemistry 56:5698-5711(2017).
RN [9]
RP X-RAY CRYSTALLOGRAPHY (2.7 ANGSTROMS), AND SUBUNIT.
RC STRAIN=K12;
RG New York structural genomix research consortium (NYSGXRC);
RT "Crystal structure of 2-methylcitrate dehydratase.";
RL Submitted (FEB-2009) to the PDB data bank.
CC -!- FUNCTION: Involved in the catabolism of short chain fatty acids (SCFA)
CC via the tricarboxylic acid (TCA)(acetyl degradation route) and via the
CC 2-methylcitrate cycle I (propionate degradation route). Catalyzes the
CC dehydration of 2-methylcitrate (2-MC) to yield the cis isomer of 2-
CC methyl-aconitate. It is also able to catalyze the dehydration of
CC citrate and the hydration of cis-aconitate at a lower rate. Due to its
CC broad substrate specificity, it seems to be responsible for the
CC residual aconitase activity of the acnAB-null mutant.
CC {ECO:0000269|PubMed:11782506, ECO:0000269|PubMed:12473114}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(2S,3S)-2-methylcitrate = 2-methyl-cis-aconitate + H2O;
CC Xref=Rhea:RHEA:17725, ChEBI:CHEBI:15377, ChEBI:CHEBI:57872,
CC ChEBI:CHEBI:58853; EC=4.2.1.79;
CC Evidence={ECO:0000269|PubMed:11782506, ECO:0000269|PubMed:12473114};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=citrate = D-threo-isocitrate; Xref=Rhea:RHEA:10336,
CC ChEBI:CHEBI:15562, ChEBI:CHEBI:16947; EC=4.2.1.3;
CC Evidence={ECO:0000269|PubMed:11782506, ECO:0000269|PubMed:12473114};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.44 mM for (2S,3S)-2-methylcitrate {ECO:0000269|PubMed:12473114};
CC -!- PATHWAY: Organic acid metabolism; propanoate degradation.
CC {ECO:0000305|PubMed:12473114}.
CC -!- PATHWAY: Carbohydrate metabolism; tricarboxylic acid cycle; isocitrate
CC from oxaloacetate: step 2/2. {ECO:0000305|PubMed:12473114}.
CC -!- SUBUNIT: Monomer. {ECO:0000269|PubMed:11782506, ECO:0000269|Ref.9}.
CC -!- INDUCTION: By propionate, but not acetate or glucose. Expression of
CC prpBCDE operon is regulated by PrpR, CRP and a variety of sugars such
CC as arabinose, galactose, glucose mannose and xylose.
CC {ECO:0000269|PubMed:12473114, ECO:0000269|PubMed:15805526,
CC ECO:0000269|PubMed:22579471}.
CC -!- DISRUPTION PHENOTYPE: Cells lacking this gene abolished the residual
CC aconitase activity of an AcnAB-null strain.
CC {ECO:0000269|PubMed:11782506}.
CC -!- MISCELLANEOUS: PrpD catalyzes an unusual syn elimination, whereas the
CC addition of water by AcnB to cis-2-methylaconitate occurs in the usual
CC anti manner. {ECO:0000269|PubMed:12473114}.
CC -!- SIMILARITY: Belongs to the PrpD family. {ECO:0000305}.
CC -!- CAUTION: There is uncertainty concerning the 2-methylcitrate
CC stereochemistry. Brock et al. report a (2S,3S) stereochemistry, but
CC Reddick et al. determined that the 2-methylcitrate has either (2S,3R)
CC or (2R,3S) stereochemistry. {ECO:0000305|PubMed:12473114,
CC ECO:0000305|PubMed:28956599}.
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DR EMBL; U73857; AAB18058.1; -; Genomic_DNA.
DR EMBL; U00096; AAC73437.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE76116.1; -; Genomic_DNA.
DR PIR; F64760; F64760.
DR RefSeq; NP_414868.1; NC_000913.3.
DR RefSeq; WP_001275859.1; NZ_LN832404.1.
DR PDB; 1SZQ; X-ray; 2.70 A; A/B=1-483.
DR PDBsum; 1SZQ; -.
DR AlphaFoldDB; P77243; -.
DR SMR; P77243; -.
DR DIP; DIP-10580N; -.
DR IntAct; P77243; 4.
DR STRING; 511145.b0334; -.
DR jPOST; P77243; -.
DR PaxDb; P77243; -.
DR PRIDE; P77243; -.
DR DNASU; 945931; -.
DR EnsemblBacteria; AAC73437; AAC73437; b0334.
DR EnsemblBacteria; BAE76116; BAE76116; BAE76116.
DR GeneID; 945931; -.
DR KEGG; ecj:JW0325; -.
DR KEGG; eco:b0334; -.
DR PATRIC; fig|1411691.4.peg.1943; -.
DR EchoBASE; EB3371; -.
DR eggNOG; COG2079; Bacteria.
DR HOGENOM; CLU_021803_1_0_6; -.
DR InParanoid; P77243; -.
DR OMA; ECTKHLG; -.
DR PhylomeDB; P77243; -.
DR BioCyc; EcoCyc:G6199-MON; -.
DR BioCyc; MetaCyc:G6199-MON; -.
DR BRENDA; 4.2.1.79; 2026.
DR SABIO-RK; P77243; -.
DR UniPathway; UPA00223; UER00718.
DR UniPathway; UPA00946; -.
DR EvolutionaryTrace; P77243; -.
DR PRO; PR:P77243; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0051537; F:2 iron, 2 sulfur cluster binding; IDA:UniProtKB.
DR GO; GO:0047547; F:2-methylcitrate dehydratase activity; IDA:EcoCyc.
DR GO; GO:0003994; F:aconitate hydratase activity; IEA:UniProtKB-EC.
DR GO; GO:0047780; F:citrate dehydratase activity; IEA:UniProtKB-EC.
DR GO; GO:0019679; P:propionate metabolic process, methylcitrate cycle; IDA:EcoliWiki.
DR GO; GO:0006099; P:tricarboxylic acid cycle; IEA:UniProtKB-UniPathway.
DR Gene3D; 1.10.4100.10; -; 1.
DR Gene3D; 3.30.1330.120; -; 1.
DR InterPro; IPR012705; 2Me_IsoCit_deHydtase_PrpD.
DR InterPro; IPR036148; MmgE/PrpD_sf.
DR InterPro; IPR042183; MmgE/PrpD_sf_1.
DR InterPro; IPR042188; MmgE/PrpD_sf_2.
DR InterPro; IPR005656; MmgE_PrpD.
DR InterPro; IPR045337; MmgE_PrpD_C.
DR InterPro; IPR045336; MmgE_PrpD_N.
DR PANTHER; PTHR16943; PTHR16943; 1.
DR Pfam; PF03972; MmgE_PrpD; 1.
DR Pfam; PF19305; MmgE_PrpD_C; 1.
DR SUPFAM; SSF103378; SSF103378; 1.
DR TIGRFAMs; TIGR02330; prpD; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Direct protein sequencing; Lyase; Reference proteome;
KW Tricarboxylic acid cycle.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:11782506"
FT CHAIN 2..483
FT /note="2-methylcitrate dehydratase"
FT /id="PRO_0000215023"
FT HELIX 14..25
FT /evidence="ECO:0007829|PDB:1SZQ"
FT HELIX 31..51
FT /evidence="ECO:0007829|PDB:1SZQ"
FT HELIX 55..58
FT /evidence="ECO:0007829|PDB:1SZQ"
FT HELIX 85..98
FT /evidence="ECO:0007829|PDB:1SZQ"
FT STRAND 107..109
FT /evidence="ECO:0007829|PDB:1SZQ"
FT HELIX 113..116
FT /evidence="ECO:0007829|PDB:1SZQ"
FT HELIX 117..133
FT /evidence="ECO:0007829|PDB:1SZQ"
FT HELIX 141..158
FT /evidence="ECO:0007829|PDB:1SZQ"
FT TURN 159..161
FT /evidence="ECO:0007829|PDB:1SZQ"
FT HELIX 165..167
FT /evidence="ECO:0007829|PDB:1SZQ"
FT HELIX 172..186
FT /evidence="ECO:0007829|PDB:1SZQ"
FT HELIX 191..202
FT /evidence="ECO:0007829|PDB:1SZQ"
FT HELIX 210..212
FT /evidence="ECO:0007829|PDB:1SZQ"
FT HELIX 220..240
FT /evidence="ECO:0007829|PDB:1SZQ"
FT TURN 247..251
FT /evidence="ECO:0007829|PDB:1SZQ"
FT TURN 253..255
FT /evidence="ECO:0007829|PDB:1SZQ"
FT HELIX 257..261
FT /evidence="ECO:0007829|PDB:1SZQ"
FT STRAND 273..275
FT /evidence="ECO:0007829|PDB:1SZQ"
FT HELIX 276..280
FT /evidence="ECO:0007829|PDB:1SZQ"
FT STRAND 286..288
FT /evidence="ECO:0007829|PDB:1SZQ"
FT TURN 291..293
FT /evidence="ECO:0007829|PDB:1SZQ"
FT HELIX 294..309
FT /evidence="ECO:0007829|PDB:1SZQ"
FT HELIX 314..316
FT /evidence="ECO:0007829|PDB:1SZQ"
FT STRAND 317..324
FT /evidence="ECO:0007829|PDB:1SZQ"
FT HELIX 326..332
FT /evidence="ECO:0007829|PDB:1SZQ"
FT HELIX 341..344
FT /evidence="ECO:0007829|PDB:1SZQ"
FT HELIX 348..358
FT /evidence="ECO:0007829|PDB:1SZQ"
FT HELIX 363..366
FT /evidence="ECO:0007829|PDB:1SZQ"
FT HELIX 368..371
FT /evidence="ECO:0007829|PDB:1SZQ"
FT HELIX 374..381
FT /evidence="ECO:0007829|PDB:1SZQ"
FT STRAND 383..387
FT /evidence="ECO:0007829|PDB:1SZQ"
FT HELIX 389..396
FT /evidence="ECO:0007829|PDB:1SZQ"
FT TURN 398..400
FT /evidence="ECO:0007829|PDB:1SZQ"
FT STRAND 405..411
FT /evidence="ECO:0007829|PDB:1SZQ"
FT STRAND 420..422
FT /evidence="ECO:0007829|PDB:1SZQ"
FT HELIX 429..431
FT /evidence="ECO:0007829|PDB:1SZQ"
FT HELIX 432..450
FT /evidence="ECO:0007829|PDB:1SZQ"
FT HELIX 453..464
FT /evidence="ECO:0007829|PDB:1SZQ"
FT HELIX 466..471
FT /evidence="ECO:0007829|PDB:1SZQ"
FT HELIX 474..478
FT /evidence="ECO:0007829|PDB:1SZQ"
FT TURN 479..481
FT /evidence="ECO:0007829|PDB:1SZQ"
SQ SEQUENCE 483 AA; 53952 MW; 965252C8983E6F64 CRC64;
MSAQINNIRP EFDREIVDIV DYVMNYEISS KVAYDTAHYC LLDTLGCGLE ALEYPACKKL
LGPIVPGTVV PNGVRVPGTQ FQLDPVQAAF NIGAMIRWLD FNDTWLAAEW GHPSDNLGGI
LATADWLSRN AVASGKAPLT MKQVLTAMIK AHEIQGCIAL ENSFNRVGLD HVLLVKVAST
AVVAEMLGLT REEILNAVSL AWVDGQSLRT YRHAPNTGTR KSWAAGDATS RAVRLALMAK
TGEMGYPSAL TAPVWGFYDV SFKGESFRFQ RPYGSYVMEN VLFKISFPAE FHSQTAVEAA
MTLYEQMQAA GKTAADIEKV TIRTHEACIR IIDKKGPLNN PADRDHCIQY MVAIPLLFGR
LTAADYEDNV AQDKRIDALR EKINCFEDPA FTADYHDPEK RAIANAITLE FTDGTRFEEV
VVEYPIGHAR RRQDGIPKLV DKFKINLARQ FPTRQQQRIL EVSLDRARLE QMPVNEYLDL
YVI
