(data stored in ACNUC7421 zone)

SWISSPROT: PRPB_SALTY

ID   PRPB_SALTY              Reviewed;         295 AA.
AC   Q56062;
DT   01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT   23-JAN-2007, sequence version 3.
DT   11-DEC-2019, entry version 123.
DE   RecName: Full=2-methylisocitrate lyase {ECO:0000303|PubMed:10482501};
DE            Short=2-MIC {ECO:0000303|PubMed:12897003};
DE            Short=MICL {ECO:0000303|PubMed:12897003};
DE            EC=4.1.3.30 {ECO:0000269|PubMed:11294638, ECO:0000269|PubMed:12897003};
DE   AltName: Full=(2R,3S)-2-methylisocitrate lyase {ECO:0000255|HAMAP-Rule:MF_01939};
GN   Name=prpB {ECO:0000303|PubMed:10482501}; OrderedLocusNames=STM0368;
OS   Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720).
OC   Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC   Enterobacteriaceae; Salmonella.
OX   NCBI_TaxID=99287;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC   STRAIN=LT2 / SGSC1412 / ATCC 700720;
RX   PubMed=9006051; DOI=10.1128/jb.179.3.928-940.1997;
RA   Horswill A.R., Escalante-Semerena J.C.;
RT   "Propionate catabolism in Salmonella typhimurium LT2: two divergently
RT   transcribed units comprise the prp locus at 8.5 centisomes, prpR encodes a
RT   member of the sigma-54 family of activators, and the prpBCDE genes
RT   constitute an operon.";
RL   J. Bacteriol. 179:928-940(1997).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=LT2 / SGSC1412 / ATCC 700720;
RX   PubMed=11677609; DOI=10.1038/35101614;
RA   McClelland M., Sanderson K.E., Spieth J., Clifton S.W., Latreille P.,
RA   Courtney L., Porwollik S., Ali J., Dante M., Du F., Hou S., Layman D.,
RA   Leonard S., Nguyen C., Scott K., Holmes A., Grewal N., Mulvaney E.,
RA   Ryan E., Sun H., Florea L., Miller W., Stoneking T., Nhan M., Waterston R.,
RA   Wilson R.K.;
RT   "Complete genome sequence of Salmonella enterica serovar Typhimurium LT2.";
RL   Nature 413:852-856(2001).
RN   [3]
RP   FUNCTION, AND DISRUPTION PHENOTYPE.
RX   PubMed=10482501;
RA   Horswill A.R., Escalante-Semerena J.C.;
RT   "Salmonella typhimurium LT2 catabolizes propionate via the 2-methylcitric
RT   acid cycle.";
RL   J. Bacteriol. 181:5615-5623(1999).
RN   [4]
RP   FUNCTION, AND CATALYTIC ACTIVITY.
RX   PubMed=11294638; DOI=10.1021/bi015503b;
RA   Horswill A.R., Escalante-Semerena J.C.;
RT   "In vitro conversion of propionate to pyruvate by Salmonella enterica
RT   enzymes: 2-methylcitrate dehydratase (PrpD) and aconitase enzymes catalyze
RT   the conversion of 2-methylcitrate to 2-methylisocitrate.";
RL   Biochemistry 40:4703-4713(2001).
RN   [5]
RP   FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, MUTAGENESIS OF
RP   ASP-58; LYS-121; ARG-122; CYS-123 AND HIS-125, COFACTOR, AND SUBUNIT.
RC   STRAIN=LT2 / SGSC1412 / ATCC 700720;
RX   PubMed=12897003; DOI=10.1128/jb.185.16.4837-4843.2003;
RA   Grimek T.L., Holden H., Rayment I., Escalante-Semerena J.C.;
RT   "Residues C123 and D58 of the 2-methylisocitrate lyase (PrpB) enzyme of
RT   Salmonella enterica are essential for catalysis.";
RL   J. Bacteriol. 185:4837-4843(2003).
RN   [6]
RP   X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) IN COMPLEX WITH SUBSTRATE AND
RP   MAGNESIUM, COFACTOR, AND SUBUNIT.
RX   PubMed=14575713; DOI=10.1016/j.bbrc.2003.09.193;
RA   Simanshu D.K., Satheshkumar P.S., Savithri H.S., Murthy M.R.;
RT   "Crystal structure of Salmonella typhimurium 2-methylisocitrate lyase
RT   (PrpB) and its complex with pyruvate and Mg(2+).";
RL   Biochem. Biophys. Res. Commun. 311:193-201(2003).
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:10482501, ECO:0000269|PubMed:11294638,
CC       ECO:0000269|PubMed:12897003}.
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:11294638, ECO:0000269|PubMed:12897003};
CC   -!- COFACTOR:
CC       Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC         Evidence={ECO:0000255|HAMAP-Rule:MF_01939,
CC         ECO:0000269|PubMed:12897003, ECO:0000269|PubMed:14575713};
CC   -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC       Kinetic parameters:
CC         KM=18 uM for 2-methylisocitrate {ECO:0000269|PubMed:12897003};
CC         Note=Kcat is 74 sec(-1) for 2-methylisocitrate lyase with 2-
CC         methylisocitrate as substrate. {ECO:0000269|PubMed:12897003};
CC       pH dependence:
CC         Optimum pH is 7.5. {ECO:0000269|PubMed:12897003};
CC       Temperature dependence:
CC         Optimum temperature is 50 degrees Celsius.
CC         {ECO:0000269|PubMed:12897003};
CC   -!- PATHWAY: Organic acid metabolism; propanoate degradation.
CC       {ECO:0000255|HAMAP-Rule:MF_01939, ECO:0000305|PubMed:9006051}.
CC   -!- SUBUNIT: Homotetramer; dimer of dimers. {ECO:0000255|HAMAP-
CC       Rule:MF_01939, ECO:0000269|PubMed:12897003,
CC       ECO:0000269|PubMed:14575713}.
CC   -!- DISRUPTION PHENOTYPE: Cells lacking this gene are unable to accumulate
CC       2-methylcitrate and 2-methyl-cis-aconitate.
CC       {ECO:0000269|PubMed:10482501}.
CC   -!- MISCELLANEOUS: In vitro, dithiothreitol (DTT) or reduced glutathione
CC       (GSH) are required for optimal activity. {ECO:0000269|PubMed:12897003}.
CC   -!- SIMILARITY: Belongs to the isocitrate lyase/PEP mutase superfamily.
CC       Methylisocitrate lyase family. {ECO:0000255|HAMAP-Rule:MF_01939}.
DR   EMBL; U51879; AAC44814.1; -; Genomic_DNA.
DR   EMBL; AE006468; AAL19322.1; -; Genomic_DNA.
DR   RefSeq; NP_459363.1; NC_003197.2.
DR   RefSeq; WP_000052224.1; NC_003197.2.
DR   PDB; 1O5Q; X-ray; 2.30 A; A/B/C/D=2-295.
DR   PDB; 1UJQ; X-ray; 2.10 A; A/B/C/D=2-295.
DR   PDBsum; 1O5Q; -.
DR   PDBsum; 1UJQ; -.
DR   SMR; Q56062; -.
DR   PaxDb; Q56062; -.
DR   PRIDE; Q56062; -.
DR   EnsemblBacteria; AAL19322; AAL19322; STM0368.
DR   GeneID; 1251887; -.
DR   KEGG; stm:STM0368; -.
DR   PATRIC; fig|99287.12.peg.390; -.
DR   eggNOG; ENOG4105CR4; Bacteria.
DR   eggNOG; COG2513; LUCA.
DR   HOGENOM; HOG000220041; -.
DR   KO; K03417; -.
DR   OMA; SMVLYPL; -.
DR   PhylomeDB; Q56062; -.
DR   BioCyc; MetaCyc:MONOMER-66; -.
DR   BioCyc; SENT99287:STM0368-MONOMER; -.
DR   UniPathway; UPA00946; -.
DR   EvolutionaryTrace; Q56062; -.
DR   Proteomes; UP000001014; 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:UniProtKB.
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;
DR   PRODOM; Q56062.
DR   SWISS-2DPAGE; Q56062.
KW   3D-structure; Lyase; Magnesium; Metal-binding; Reference proteome.
FT   INIT_MET        1
FT                   /note="Removed"
FT                   /evidence="ECO:0000305"
FT   CHAIN           2..295
FT                   /note="2-methylisocitrate lyase"
FT                   /id="PRO_0000068816"
FT   REGION          45..47
FT                   /note="Substrate binding"
FT                   /evidence="ECO:0000269|PubMed:14575713"
FT   REGION          123..124
FT                   /note="Substrate binding"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01939"
FT   REGION          210..212
FT                   /note="Substrate binding"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01939"
FT   METAL           85
FT                   /note="Magnesium"
FT                   /evidence="ECO:0000269|PubMed:14575713"
FT   METAL           87
FT                   /note="Magnesium"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01939"
FT   BINDING         158
FT                   /note="Substrate"
FT                   /evidence="ECO:0000269|PubMed:14575713"
FT   BINDING         188
FT                   /note="Substrate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01939"
FT   BINDING         241
FT                   /note="Substrate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01939"
FT   BINDING         270
FT                   /note="Substrate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01939"
FT   MUTAGEN         58
FT                   /note="D->A: Inactive. Retains the same oligomeric state of
FT                   the wild-type."
FT                   /evidence="ECO:0000269|PubMed:12897003"
FT   MUTAGEN         121
FT                   /note="K->A: 1000-fold decrease in the catalytic
FT                   efficiency. Retains the same oligomeric state of the wild-
FT                   type."
FT                   /evidence="ECO:0000269|PubMed:12897003"
FT   MUTAGEN         122
FT                   /note="R->K: 2-fold decrease in the catalytic efficiency.
FT                   Retains the same oligomeric state of the wild-type."
FT                   /evidence="ECO:0000269|PubMed:12897003"
FT   MUTAGEN         123
FT                   /note="C->A: Inactive. Retains the same oligomeric state of
FT                   the wild-type."
FT                   /evidence="ECO:0000269|PubMed:12897003"
FT   MUTAGEN         125
FT                   /note="H->A: 750-fold decrease in the catalytic efficiency.
FT                   Retains the same oligomeric state of the wild-type."
FT                   /evidence="ECO:0000269|PubMed:12897003"
FT   HELIX           6..16
FT                   /evidence="ECO:0000244|PDB:1UJQ"
FT   STRAND          17..24
FT                   /evidence="ECO:0000244|PDB:1UJQ"
FT   HELIX           28..37
FT                   /evidence="ECO:0000244|PDB:1UJQ"
FT   STRAND          40..44
FT                   /evidence="ECO:0000244|PDB:1UJQ"
FT   HELIX           46..51
FT                   /evidence="ECO:0000244|PDB:1UJQ"
FT   STRAND          58..60
FT                   /evidence="ECO:0000244|PDB:1UJQ"
FT   HELIX           64..77
FT                   /evidence="ECO:0000244|PDB:1UJQ"
FT   STRAND          82..85
FT                   /evidence="ECO:0000244|PDB:1UJQ"
FT   STRAND          90..93
FT                   /evidence="ECO:0000244|PDB:1UJQ"
FT   HELIX           94..106
FT                   /evidence="ECO:0000244|PDB:1UJQ"
FT   STRAND          110..115
FT                   /evidence="ECO:0000244|PDB:1UJQ"
FT   HELIX           134..147
FT                   /evidence="ECO:0000244|PDB:1UJQ"
FT   STRAND          153..159
FT                   /evidence="ECO:0000244|PDB:1UJQ"
FT   HELIX           161..165
FT                   /evidence="ECO:0000244|PDB:1UJQ"
FT   HELIX           167..179
FT                   /evidence="ECO:0000244|PDB:1UJQ"
FT   STRAND          183..187
FT                   /evidence="ECO:0000244|PDB:1UJQ"
FT   HELIX           193..203
FT                   /evidence="ECO:0000244|PDB:1UJQ"
FT   STRAND          207..210
FT                   /evidence="ECO:0000244|PDB:1UJQ"
FT   STRAND          213..217
FT                   /evidence="ECO:0000244|PDB:1UJQ"
FT   HELIX           222..227
FT                   /evidence="ECO:0000244|PDB:1UJQ"
FT   STRAND          232..237
FT                   /evidence="ECO:0000244|PDB:1UJQ"
FT   HELIX           238..257
FT                   /evidence="ECO:0000244|PDB:1UJQ"
FT   STRAND          258..260
FT                   /evidence="ECO:0000244|PDB:1O5Q"
FT   HELIX           261..266
FT                   /evidence="ECO:0000244|PDB:1UJQ"
FT   HELIX           270..276
FT                   /evidence="ECO:0000244|PDB:1UJQ"
FT   HELIX           279..285
FT                   /evidence="ECO:0000244|PDB:1UJQ"
SQ   SEQUENCE   295 AA;  32000 MW;  08AD38D071B98F1D CRC64;
     MSLHSPGQAF RAALAKENPL QIVGAINANH ALLAQRAGYQ AIYLSGGGVA AGSLGLPDLG
     ISTLDDVLTD IRRITDVCPL PLLVDADIGF GSSAFNVART VKSIAKAGAA ALHIEDQVGA
     KRCGHRPNKA IVSKEEMVDR IRAAVDARTD PNFVIMARTD ALAVEGLEAA LDRAQAYVDA
     GADMLFPEAI TELSMYRRFA DVAQVPILAN ITEFGATPLF TTDELRSAHV AMALYPLSAF
     RAMNRAAEKV YTVLRQEGTQ KNVIDIMQTR NELYESINYY QFEEKLDALY RNKKS
//

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