RIDA_SALTY
ID RIDA_SALTY Reviewed; 128 AA.
AC Q7CP78; Q7BS56;
DT 21-MAR-2012, integrated into UniProtKB/Swiss-Prot.
DT 05-JUL-2004, sequence version 1.
DT 03-AUG-2022, entry version 97.
DE RecName: Full=2-iminobutanoate/2-iminopropanoate deaminase;
DE EC=3.5.99.10 {ECO:0000269|PubMed:22094463};
DE AltName: Full=Enamine/imine deaminase {ECO:0000303|PubMed:22094463};
GN Name=ridA {ECO:0000303|PubMed:22094463}; Synonyms=yjgF;
GN OrderedLocusNames=STM4458;
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], FUNCTION IN THE BIOSYNTHESIS OF
RP ISOLEUCINE, AND DISRUPTION PHENOTYPE.
RC STRAIN=LT2;
RX PubMed=9851994; DOI=10.1128/jb.180.24.6519-6528.1998;
RA Enos-Berlage J.L., Langendorf M.J., Downs D.M.;
RT "Complex metabolic phenotypes caused by a mutation in yjgF, encoding a
RT member of the highly conserved YER057c/YjgF family of proteins.";
RL J. Bacteriol. 180:6519-6528(1998).
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 IN THE BIOSYNTHESIS OF ISOLEUCINE, AND DISRUPTION PHENOTYPE.
RC STRAIN=LT2;
RX PubMed=18296521; DOI=10.1128/jb.01700-07;
RA Christopherson M.R., Schmitz G.E., Downs D.M.;
RT "YjgF is required for isoleucine biosynthesis when Salmonella enterica is
RT grown on pyruvate medium.";
RL J. Bacteriol. 190:3057-3062(2008).
RN [4]
RP DISRUPTION PHENOTYPE.
RC STRAIN=LT2;
RX PubMed=20817725; DOI=10.1074/jbc.m110.160515;
RA Lambrecht J.A., Browne B.A., Downs D.M.;
RT "Members of the YjgF/YER057c/UK114 family of proteins inhibit
RT phosphoribosylamine synthesis in vitro.";
RL J. Biol. Chem. 285:34401-34407(2010).
RN [5]
RP FUNCTION AS A DEAMINASE, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES,
RP MUTAGENESIS OF TYR-17; ARG-105 AND GLU-120, SUBSTRATE SPECIFICITY, AND
RP NOMENCLATURE.
RC STRAIN=LT2;
RX PubMed=22094463; DOI=10.1074/jbc.m111.304477;
RA Lambrecht J.A., Flynn J.M., Downs D.M.;
RT "The conserved YjgF protein family deaminates enamine/imine intermediates
RT of pyridoxal-5'-phosphate (PLP)-dependent enzyme reactions.";
RL J. Biol. Chem. 287:3454-3461(2012).
CC -!- FUNCTION: Accelerates the release of ammonia from reactive
CC enamine/imine intermediates of the PLP-dependent threonine dehydratase
CC (IlvA) in the low water environment of the cell. It catalyzes the
CC deamination of enamine/imine intermediates to yield 2-ketobutyrate and
CC ammonia. It is required for the detoxification of reactive
CC intermediates of IlvA due to their highly nucleophilic abilities and to
CC avoid they are captured by anthranilate phosphoribosyltransferase
CC (TrpD) to generate PRA, an intermediate in the alternative pyrimidine
CC biosynthetic (APB) pathway. Also required for full activity of IlvE
CC which is involved in the isoleucine biosynthesis. RidA also accelerates
CC the release of pyruvate produced by IlvA from L-serine.
CC {ECO:0000269|PubMed:18296521, ECO:0000269|PubMed:22094463,
CC ECO:0000269|PubMed:9851994}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2-iminobutanoate + H2O = 2-oxobutanoate + NH4(+);
CC Xref=Rhea:RHEA:39975, ChEBI:CHEBI:15377, ChEBI:CHEBI:16763,
CC ChEBI:CHEBI:28938, ChEBI:CHEBI:76545; EC=3.5.99.10;
CC Evidence={ECO:0000269|PubMed:22094463};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2-iminopropanoate + H2O = NH4(+) + pyruvate;
CC Xref=Rhea:RHEA:40671, ChEBI:CHEBI:15361, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:28938, ChEBI:CHEBI:44400; EC=3.5.99.10;
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC pH dependence:
CC Optimum pH is around 9 due to the greater stability of the
CC enamine/imine intermediate at high pH. {ECO:0000269|PubMed:22094463};
CC -!- PATHWAY: Amino-acid biosynthesis; L-isoleucine biosynthesis; 2-
CC oxobutanoate from L-threonine. {ECO:0000269|PubMed:18296521,
CC ECO:0000269|PubMed:9851994}.
CC -!- SUBUNIT: Homotrimer. {ECO:0000250|UniProtKB:P0AF93}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000305}.
CC -!- DISRUPTION PHENOTYPE: Cells lacking this gene appear to be compromised
CC in their ability to synthesize isoleucine. Mutation results in the
CC partial block of at least one step in isoleucine biosynthesis
CC subsequent to the reaction catalyzed by threonine deaminase (IlvA).
CC Mutation is required for the dependence of the PurF-independent
CC alternative pyrimidine biosynthesis (APB) pathway of thiamine upon the
CC oxidative pentose phosphate pathway. {ECO:0000269|PubMed:18296521,
CC ECO:0000269|PubMed:20817725, ECO:0000269|PubMed:9851994}.
CC -!- SIMILARITY: Belongs to the RutC family. {ECO:0000305}.
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DR EMBL; AF095578; AAD22768.1; -; Genomic_DNA.
DR EMBL; AE006468; AAL23277.1; -; Genomic_DNA.
DR RefSeq; NP_463318.1; NC_003197.2.
DR RefSeq; WP_000047544.1; NC_003197.2.
DR AlphaFoldDB; Q7CP78; -.
DR SMR; Q7CP78; -.
DR STRING; 99287.STM4458; -.
DR PaxDb; Q7CP78; -.
DR EnsemblBacteria; AAL23277; AAL23277; STM4458.
DR GeneID; 1255984; -.
DR GeneID; 64171784; -.
DR GeneID; 67518181; -.
DR KEGG; stm:STM4458; -.
DR PATRIC; fig|99287.12.peg.4691; -.
DR HOGENOM; CLU_100715_7_1_6; -.
DR OMA; GSYFKEP; -.
DR PhylomeDB; Q7CP78; -.
DR BioCyc; MetaCyc:STM4458-MON; -.
DR BioCyc; SENT99287:STM4458-MON; -.
DR BRENDA; 3.5.99.10; 5542.
DR PRO; PR:Q7CP78; -.
DR Proteomes; UP000001014; Chromosome.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0120242; F:2-iminobutanoate deaminase activity; IDA:UniProtKB.
DR GO; GO:0120243; F:2-iminopropanoate deaminase activity; IEA:RHEA.
DR GO; GO:0019239; F:deaminase activity; IBA:GO_Central.
DR GO; GO:0009097; P:isoleucine biosynthetic process; IMP:UniProtKB.
DR GO; GO:1901565; P:organonitrogen compound catabolic process; IBA:GO_Central.
DR GO; GO:0009636; P:response to toxic substance; IEA:UniProtKB-KW.
DR Gene3D; 3.30.1330.40; -; 1.
DR InterPro; IPR006056; RidA.
DR InterPro; IPR019897; RidA_CS.
DR InterPro; IPR035959; RutC-like_sf.
DR InterPro; IPR006175; YjgF/YER057c/UK114.
DR PANTHER; PTHR11803; PTHR11803; 1.
DR Pfam; PF01042; Ribonuc_L-PSP; 1.
DR SUPFAM; SSF55298; SSF55298; 1.
DR TIGRFAMs; TIGR00004; TIGR00004; 1.
DR PROSITE; PS01094; UPF0076; 1.
PE 1: Evidence at protein level;
KW Amino-acid biosynthesis; Branched-chain amino acid biosynthesis; Cytoplasm;
KW Detoxification; Hydrolase; Isoleucine biosynthesis; Reference proteome.
FT CHAIN 1..128
FT /note="2-iminobutanoate/2-iminopropanoate deaminase"
FT /id="PRO_0000416001"
FT BINDING 105
FT /ligand="substrate"
FT /evidence="ECO:0000305|PubMed:22094463"
FT SITE 17
FT /note="Stabilizes the substrate"
FT /evidence="ECO:0000305|PubMed:22094463"
FT SITE 120
FT /note="Important for catalytic activity at high pH"
FT /evidence="ECO:0000269|PubMed:22094463"
FT MUTAGEN 17
FT /note="Y->F: Deaminase activity is defective. At pH 8,
FT strongly reduces the increase in rate of 2-ketobutyrate
FT formation over the rate of IlvA alone. At pH 9.5,
FT moderately reduces the increase in rate of 2-ketobutyrate
FT formation over the rate of IlvA alone."
FT /evidence="ECO:0000269|PubMed:22094463"
FT MUTAGEN 105
FT /note="R->A: Deaminase activity is defective. At pH 8 and
FT 9.5, strongly reduces the increase in rate of 2-
FT ketobutyrate formation over the rate of IlvA alone."
FT /evidence="ECO:0000269|PubMed:22094463"
FT MUTAGEN 120
FT /note="E->A: Deaminase activity is defective. At pH 8,
FT moderately reduces the increase in rate of 2-ketobutyrate
FT formation over the rate of IlvA alone. At pH 9.5, strongly
FT reduces the increase in rate of 2-ketobutyrate formation
FT over the rate of IlvA alone."
FT /evidence="ECO:0000269|PubMed:22094463"
FT MUTAGEN 120
FT /note="E->K: Deaminase activity is defective. At pH 8,
FT moderately reduces the increase in rate of 2-ketobutyrate
FT formation over the rate of IlvA alone. At pH 9.5, strongly
FT reduces the increase in rate of 2-ketobutyrate formation
FT over the rate of IlvA alone."
FT /evidence="ECO:0000269|PubMed:22094463"
SQ SEQUENCE 128 AA; 13576 MW; 9E66F1287DE67B1A CRC64;
MSKTIATENA PAAIGPYVQG VDLGSMVITS GQIPVDPKTG AVAEDVSAQA RQSLENVKAI
VEAAGLKVGD IVKTTVFVKD LNDFATVNAT YEAFFTEHNA TFPARSCVEV ARLPKDVKIE
IEAIAVRR
