PRPB_ECOLI
ID PRPB_ECOLI Reviewed; 296 AA.
AC P77541; Q2MC92;
DT 01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 3.
DT 03-AUG-2022, entry version 158.
DE RecName: Full=2-methylisocitrate lyase {ECO:0000303|PubMed:11422389};
DE Short=2-MIC {ECO:0000303|PubMed:15723538};
DE Short=MICL {ECO:0000303|PubMed:15723538};
DE EC=4.1.3.30 {ECO:0000269|PubMed:11422389, ECO:0000269|PubMed:15723538};
DE AltName: Full=(2R,3S)-2-methylisocitrate lyase {ECO:0000303|PubMed:11422389};
GN Name=prpB {ECO:0000255|HAMAP-Rule:MF_01939}; Synonyms=yahQ;
GN OrderedLocusNames=b0331, JW0323;
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 2-12, AND PATHWAY.
RX PubMed=9325432; DOI=10.1007/s002030050518;
RA Textor S., Wendisch V.F., de Graaf A.A., Mueller U., Linder M.I.,
RA Linder D., Buckel W.;
RT "Propionate oxidation in Escherichia coli: evidence for operation of a
RT methylcitrate cycle in bacteria.";
RL Arch. Microbiol. 168:428-436(1997).
RN [5]
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, AND COFACTOR.
RX PubMed=11422389; DOI=10.1046/j.1432-1327.2001.02262.x;
RA Brock M., Darley D., Textor S., Buckel W.;
RT "2-Methylisocitrate lyases from the bacterium Escherichia coli and the
RT filamentous fungus Aspergillus nidulans: characterization and comparison of
RT both enzymes.";
RL Eur. J. Biochem. 268:3577-3586(2001).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (1.90 ANGSTROMS) OF 2-295 IN COMPLEX WITH MAGNESIUM,
RP COFACTOR, AND SUBUNIT.
RX PubMed=12706720; DOI=10.1016/s0022-2836(03)00358-9;
RA Grimm C., Evers A., Brock M., Maerker C., Klebe G., Buckel W., Reuter K.;
RT "Crystal structure of 2-methylisocitrate lyase (PrpB) from Escherichia coli
RT and modelling of its ligand bound active centre.";
RL J. Mol. Biol. 328:609-621(2003).
RN [7]
RP X-RAY CRYSTALLOGRAPHY (1.60 ANGSTROMS) OF 2-295 IN COMPLEX WITH SUBSTRATE
RP AND MAGNESIUM, FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES,
RP MUTAGENESIS OF CYS-123, COFACTOR, SUBUNIT, SUBSTRATE SPECIFICITY, AND
RP REACTION MECHANISM.
RX PubMed=15723538; DOI=10.1021/bi0479712;
RA Liu S., Lu Z., Han Y., Melamud E., Dunaway-Mariano D., Herzberg O.;
RT "Crystal structures of 2-methylisocitrate lyase in complex with product and
RT with isocitrate inhibitor provide insight into lyase substrate specificity,
RT catalysis and evolution.";
RL Biochemistry 44:2949-2962(2005).
CC -!- FUNCTION: Involved in the catabolism of short chain fatty acids (SCFA)
CC via the 2-methylcitrate cycle I (propionate degradation route).
CC Catalyzes the thermodynamically favored C-C bond cleavage of (2R,3S)-2-
CC methylisocitrate to yield pyruvate and succinate via an alpha-carboxy-
CC carbanion intermediate. {ECO:0000255|HAMAP-Rule:MF_01939,
CC ECO:0000269|PubMed:11422389, ECO:0000269|PubMed:15723538}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate = pyruvate +
CC succinate; Xref=Rhea:RHEA:16809, ChEBI:CHEBI:15361,
CC ChEBI:CHEBI:30031, ChEBI:CHEBI:57429; EC=4.1.3.30;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01939,
CC ECO:0000269|PubMed:11422389, ECO:0000269|PubMed:15723538};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01939,
CC ECO:0000269|PubMed:11422389, ECO:0000269|PubMed:12706720,
CC ECO:0000269|PubMed:15723538};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=35 uM for magnesium {ECO:0000269|PubMed:11422389,
CC ECO:0000269|PubMed:15723538};
CC KM=19 uM for threo-2-methylisocitrate (a mixture of (2R,3S)- and
CC (2S,3R)-2-methylisocitrate in presence of 2 mM magnesium at pH 7 and
CC 30 degrees Celsius) {ECO:0000269|PubMed:11422389,
CC ECO:0000269|PubMed:15723538};
CC Note=kcat is 12 sec(-1) for methylisocitrate lyase with threo-2-
CC methylisocitrate as substrate (mixture of (2R,3S)- and (2S,3R)-2-
CC methylisocitrate at pH 7 and 30 degrees Celsius).
CC {ECO:0000269|PubMed:15723538};
CC -!- PATHWAY: Organic acid metabolism; propanoate degradation.
CC {ECO:0000255|HAMAP-Rule:MF_01939, ECO:0000305|PubMed:9325432}.
CC -!- SUBUNIT: Homotetramer; dimer of dimers. {ECO:0000255|HAMAP-
CC Rule:MF_01939, ECO:0000269|PubMed:12706720,
CC ECO:0000269|PubMed:15723538}.
CC -!- SIMILARITY: Belongs to the isocitrate lyase/PEP mutase superfamily.
CC Methylisocitrate lyase family. {ECO:0000255|HAMAP-Rule:MF_01939,
CC ECO:0000305}.
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DR EMBL; U73857; AAB18055.1; -; Genomic_DNA.
DR EMBL; U00096; AAC73434.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE76114.1; -; Genomic_DNA.
DR PIR; C64760; C64760.
DR RefSeq; NP_414865.1; NC_000913.3.
DR RefSeq; WP_000052206.1; NZ_LN832404.1.
DR PDB; 1MUM; X-ray; 1.90 A; A/B=2-296.
DR PDB; 1OQF; X-ray; 1.93 A; A/B=2-296.
DR PDB; 1XG3; X-ray; 1.90 A; A/B/C/D=2-296.
DR PDB; 1XG4; X-ray; 1.60 A; A/B/C/D=2-296.
DR PDBsum; 1MUM; -.
DR PDBsum; 1OQF; -.
DR PDBsum; 1XG3; -.
DR PDBsum; 1XG4; -.
DR AlphaFoldDB; P77541; -.
DR SMR; P77541; -.
DR BioGRID; 4259808; 9.
DR IntAct; P77541; 12.
DR STRING; 511145.b0331; -.
DR DrugBank; DB01727; Isocitric Acid.
DR jPOST; P77541; -.
DR PaxDb; P77541; -.
DR PRIDE; P77541; -.
DR EnsemblBacteria; AAC73434; AAC73434; b0331.
DR EnsemblBacteria; BAE76114; BAE76114; BAE76114.
DR GeneID; 944990; -.
DR KEGG; ecj:JW0323; -.
DR KEGG; eco:b0331; -.
DR PATRIC; fig|1411691.4.peg.1945; -.
DR EchoBASE; EB3370; -.
DR eggNOG; COG2513; Bacteria.
DR HOGENOM; CLU_027389_3_2_6; -.
DR InParanoid; P77541; -.
DR OMA; QTELWNK; -.
DR PhylomeDB; P77541; -.
DR BioCyc; EcoCyc:G6196-MON; -.
DR BioCyc; MetaCyc:G6196-MON; -.
DR BRENDA; 4.1.3.30; 2026.
DR SABIO-RK; P77541; -.
DR UniPathway; UPA00946; -.
DR EvolutionaryTrace; P77541; -.
DR PRO; PR:P77541; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0000287; F:magnesium ion binding; IDA:UniProtKB.
DR GO; GO:0046421; F:methylisocitrate lyase activity; IDA:UniProtKB.
DR GO; GO:0019629; P:propionate catabolic process, 2-methylcitrate cycle; IDA:EcoCyc.
DR CDD; cd00377; ICL_PEPM; 1.
DR Gene3D; 3.20.20.60; -; 1.
DR HAMAP; MF_01939; PrpB; 1.
DR InterPro; IPR039556; ICL/PEPM.
DR InterPro; IPR018523; Isocitrate_lyase_ph_CS.
DR InterPro; IPR012695; PrpB.
DR InterPro; IPR015813; Pyrv/PenolPyrv_Kinase-like_dom.
DR InterPro; IPR040442; Pyrv_Kinase-like_dom_sf.
DR SUPFAM; SSF51621; SSF51621; 1.
DR TIGRFAMs; TIGR02317; prpB; 1.
DR PROSITE; PS00161; ISOCITRATE_LYASE; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Direct protein sequencing; Lyase; Magnesium; Metal-binding;
KW Reference proteome.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:15723538,
FT ECO:0000269|PubMed:9325432"
FT CHAIN 2..296
FT /note="2-methylisocitrate lyase"
FT /id="PRO_0000068815"
FT BINDING 45..47
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01939,
FT ECO:0000269|PubMed:15723538"
FT BINDING 85
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01939,
FT ECO:0000269|PubMed:12706720, ECO:0000269|PubMed:15723538"
FT BINDING 87
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01939,
FT ECO:0000269|PubMed:12706720, ECO:0000269|PubMed:15723538"
FT BINDING 123..124
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01939,
FT ECO:0000269|PubMed:15723538"
FT BINDING 158
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01939,
FT ECO:0000269|PubMed:15723538"
FT BINDING 188
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01939,
FT ECO:0000269|PubMed:15723538"
FT BINDING 210..212
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01939,
FT ECO:0000269|PubMed:15723538"
FT BINDING 241
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01939,
FT ECO:0000269|PubMed:15723538"
FT BINDING 270
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01939,
FT ECO:0000269|PubMed:15723538"
FT MUTAGEN 123
FT /note="C->S: Inactive."
FT /evidence="ECO:0000269|PubMed:15723538"
FT HELIX 6..16
FT /evidence="ECO:0007829|PDB:1XG4"
FT STRAND 17..24
FT /evidence="ECO:0007829|PDB:1XG4"
FT HELIX 28..36
FT /evidence="ECO:0007829|PDB:1XG4"
FT STRAND 42..44
FT /evidence="ECO:0007829|PDB:1XG4"
FT HELIX 46..51
FT /evidence="ECO:0007829|PDB:1XG4"
FT TURN 52..54
FT /evidence="ECO:0007829|PDB:1XG3"
FT STRAND 58..60
FT /evidence="ECO:0007829|PDB:1XG4"
FT HELIX 64..77
FT /evidence="ECO:0007829|PDB:1XG4"
FT STRAND 82..85
FT /evidence="ECO:0007829|PDB:1XG4"
FT STRAND 90..93
FT /evidence="ECO:0007829|PDB:1XG4"
FT HELIX 94..107
FT /evidence="ECO:0007829|PDB:1XG4"
FT STRAND 110..115
FT /evidence="ECO:0007829|PDB:1XG4"
FT STRAND 126..128
FT /evidence="ECO:0007829|PDB:1XG4"
FT HELIX 134..147
FT /evidence="ECO:0007829|PDB:1XG4"
FT STRAND 153..159
FT /evidence="ECO:0007829|PDB:1XG4"
FT HELIX 162..165
FT /evidence="ECO:0007829|PDB:1XG4"
FT HELIX 167..179
FT /evidence="ECO:0007829|PDB:1XG4"
FT STRAND 183..187
FT /evidence="ECO:0007829|PDB:1XG4"
FT HELIX 193..203
FT /evidence="ECO:0007829|PDB:1XG4"
FT STRAND 207..210
FT /evidence="ECO:0007829|PDB:1XG4"
FT STRAND 213..217
FT /evidence="ECO:0007829|PDB:1XG4"
FT HELIX 222..227
FT /evidence="ECO:0007829|PDB:1XG4"
FT STRAND 231..237
FT /evidence="ECO:0007829|PDB:1XG4"
FT HELIX 238..257
FT /evidence="ECO:0007829|PDB:1XG4"
FT STRAND 258..260
FT /evidence="ECO:0007829|PDB:1XG4"
FT HELIX 261..266
FT /evidence="ECO:0007829|PDB:1XG4"
FT HELIX 270..276
FT /evidence="ECO:0007829|PDB:1XG4"
FT HELIX 279..287
FT /evidence="ECO:0007829|PDB:1XG4"
SQ SEQUENCE 296 AA; 32135 MW; 2AA3DAE3F84472F3 CRC64;
MSLHSPGKAF RAALTKENPL QIVGTINANH ALLAQRAGYQ AIYLSGGGVA AGSLGLPDLG
ISTLDDVLTD IRRITDVCSL PLLVDADIGF GSSAFNVART VKSMIKAGAA GLHIEDQVGA
KRCGHRPNKA IVSKEEMVDR IRAAVDAKTD PDFVIMARTD ALAVEGLDAA IERAQAYVEA
GAEMLFPEAI TELAMYRQFA DAVQVPILAN ITEFGATPLF TTDELRSAHV AMALYPLSAF
RAMNRAAEHV YNVLRQEGTQ KSVIDTMQTR NELYESINYY QYEEKLDNLF ARSQVK
