RIDA_BACSU
ID RIDA_BACSU Reviewed; 125 AA.
AC P37552;
DT 01-OCT-1994, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 3.
DT 03-AUG-2022, entry version 144.
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=yabJ;
GN OrderedLocusNames=BSU00480;
OS Bacillus subtilis (strain 168).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus.
OX NCBI_TaxID=224308;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=168;
RX PubMed=7584024; DOI=10.1093/dnares/1.1.1;
RA Ogasawara N., Nakai S., Yoshikawa H.;
RT "Systematic sequencing of the 180 kilobase region of the Bacillus subtilis
RT chromosome containing the replication origin.";
RL DNA Res. 1:1-14(1994).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=168;
RX PubMed=9384377; DOI=10.1038/36786;
RA Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V.,
RA Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R.,
RA Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S.,
RA Bruschi C.V., Caldwell B., Capuano V., Carter N.M., Choi S.-K.,
RA Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F.,
RA Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D.,
RA Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M.,
RA Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P.,
RA Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K.,
RA Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S.,
RA Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y.,
RA Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G.,
RA Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J.,
RA Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C.,
RA Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S.,
RA Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B.,
RA Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S.,
RA Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M.,
RA Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y.,
RA Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J.,
RA Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A.,
RA Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M.,
RA Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S.,
RA Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E.,
RA Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K.,
RA Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E.,
RA Yoshikawa H., Danchin A.;
RT "The complete genome sequence of the Gram-positive bacterium Bacillus
RT subtilis.";
RL Nature 390:249-256(1997).
RN [3]
RP PRELIMINARY FUNCTIONAL ASSIGNMENT.
RX PubMed=10368157; DOI=10.1128/jb.181.12.3810-3815.1999;
RA Rappu P., Shin B.S., Zalkin H., Maentsaelae P.;
RT "A role for a highly conserved protein of unknown function in regulation of
RT Bacillus subtilis purA by the purine repressor.";
RL J. Bacteriol. 181:3810-3815(1999).
RN [4]
RP REVISION OF FUNCTION.
RX PubMed=14594850; DOI=10.1128/jb.185.22.6728-6731.2003;
RA Rappu P., Pullinen T., Mantsaelae P.;
RT "In vivo effect of mutations at the PRPP binding site of the Bacillus
RT subtilis purine repressor.";
RL J. Bacteriol. 185:6728-6731(2003).
RN [5]
RP FUNCTION AS A DEAMINASE, AND CATALYTIC ACTIVITY.
RC STRAIN=168;
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).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS), PROTEIN SEQUENCE OF N-TERMINUS, AND
RP SUBUNIT.
RX PubMed=10557275; DOI=10.1073/pnas.96.23.13074;
RA Sinha S., Rappu P., Lange S.C., Maentsaelae P., Zalkin H., Smith J.L.;
RT "Crystal structure of Bacillus subtilis YabJ, a purine regulatory protein
RT and member of the highly conserved YjgF family.";
RL Proc. Natl. Acad. Sci. U.S.A. 96:13074-13079(1999).
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.
CC Involved in the isoleucine biosynthesis. {ECO:0000269|PubMed:22094463}.
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 -!- PATHWAY: Amino-acid biosynthesis; L-isoleucine biosynthesis; 2-
CC oxobutanoate from L-threonine. {ECO:0000250|UniProtKB:Q7CP78}.
CC -!- SUBUNIT: Homotrimer. {ECO:0000269|PubMed:10557275}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the RutC family. {ECO:0000305}.
CC -!- CAUTION: Was originally (PubMed:10368157) thought to have a role in the
CC purine repressor-mediated regulation of purA or the pur operon. The
CC effect of yabJ (now ridA) on regulation of purA was due to the
CC orientation of the marker gene downstream of purR in the yabJ mutant
CC strain used in PubMed:10368157. {ECO:0000269|PubMed:14594850,
CC ECO:0000305|PubMed:10368157}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; D26185; BAA05283.1; -; Genomic_DNA.
DR EMBL; AL009126; CAB11824.1; -; Genomic_DNA.
DR PIR; S66077; S66077.
DR RefSeq; NP_387929.1; NC_000964.3.
DR RefSeq; WP_003226738.1; NZ_JNCM01000028.1.
DR PDB; 1QD9; X-ray; 1.70 A; A/B/C=2-125.
DR PDBsum; 1QD9; -.
DR AlphaFoldDB; P37552; -.
DR SMR; P37552; -.
DR STRING; 224308.BSU00480; -.
DR jPOST; P37552; -.
DR PaxDb; P37552; -.
DR PRIDE; P37552; -.
DR EnsemblBacteria; CAB11824; CAB11824; BSU_00480.
DR GeneID; 50135228; -.
DR GeneID; 936988; -.
DR KEGG; bsu:BSU00480; -.
DR PATRIC; fig|224308.179.peg.48; -.
DR eggNOG; COG0251; Bacteria.
DR InParanoid; P37552; -.
DR OMA; GSYFKEP; -.
DR PhylomeDB; P37552; -.
DR BioCyc; BSUB:BSU00480-MON; -.
DR BRENDA; 3.5.99.10; 658.
DR EvolutionaryTrace; P37552; -.
DR Proteomes; UP000001570; 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:0046360; P:2-oxobutyrate biosynthetic process; IDA:CACAO.
DR GO; GO:0009097; P:isoleucine biosynthetic process; IEA:UniProtKB-KW.
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 3D-structure; Amino-acid biosynthesis;
KW Branched-chain amino acid biosynthesis; Cytoplasm; Detoxification;
KW Direct protein sequencing; Hydrolase; Isoleucine biosynthesis;
KW Reference proteome.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:10557275"
FT CHAIN 2..125
FT /note="2-iminobutanoate/2-iminopropanoate deaminase"
FT /id="PRO_0000170330"
FT BINDING 102
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q7CP78"
FT SITE 17
FT /note="Stabilizes the substrate"
FT /evidence="ECO:0000250|UniProtKB:Q7CP78"
FT SITE 117
FT /note="Important for catalytic activity at high pH"
FT /evidence="ECO:0000250|UniProtKB:Q7CP78"
FT STRAND 3..5
FT /evidence="ECO:0007829|PDB:1QD9"
FT STRAND 18..23
FT /evidence="ECO:0007829|PDB:1QD9"
FT STRAND 26..29
FT /evidence="ECO:0007829|PDB:1QD9"
FT HELIX 46..63
FT /evidence="ECO:0007829|PDB:1QD9"
FT HELIX 68..70
FT /evidence="ECO:0007829|PDB:1QD9"
FT STRAND 71..79
FT /evidence="ECO:0007829|PDB:1QD9"
FT HELIX 81..83
FT /evidence="ECO:0007829|PDB:1QD9"
FT HELIX 84..94
FT /evidence="ECO:0007829|PDB:1QD9"
FT STRAND 95..97
FT /evidence="ECO:0007829|PDB:1QD9"
FT STRAND 101..106
FT /evidence="ECO:0007829|PDB:1QD9"
FT HELIX 111..113
FT /evidence="ECO:0007829|PDB:1QD9"
FT STRAND 115..123
FT /evidence="ECO:0007829|PDB:1QD9"
SQ SEQUENCE 125 AA; 13654 MW; 93A9721B82ED3490 CRC64;
MTKAVHTKHA PAAIGPYSQG IIVNNMFYSS GQIPLTPSGE MVNGDIKEQT HQVFSNLKAV
LEEAGASFET VVKATVFIAD MEQFAEVNEV YGQYFDTHKP ARSCVEVARL PKDALVEIEV
IALVK
