RIDA_RAT
ID RIDA_RAT Reviewed; 137 AA.
AC P52759; O35262; Q9WUV8;
DT 01-OCT-1996, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 3.
DT 03-AUG-2022, entry version 152.
DE RecName: Full=2-iminobutanoate/2-iminopropanoate deaminase {ECO:0000250|UniProtKB:P52758};
DE EC=3.5.99.10 {ECO:0000250|UniProtKB:P52758};
DE AltName: Full=Liver perchloric acid-soluble protein {ECO:0000303|PubMed:10400702, ECO:0000303|PubMed:8530410};
DE Short=L-PSP {ECO:0000303|PubMed:10400702};
DE AltName: Full=Reactive intermediate imine deaminase A homolog {ECO:0000312|RGD:70940};
DE AltName: Full=Translation inhibitor L-PSP ribonuclease {ECO:0000303|PubMed:10400702};
DE AltName: Full=UK114 antigen homolog {ECO:0000305|PubMed:17416349};
DE AltName: Full=rp14.5 {ECO:0000303|PubMed:11003673};
GN Name=Rida {ECO:0000312|RGD:70940};
GN Synonyms=Psp1 {ECO:0000312|EMBL:BAA08359.1};
OS Rattus norvegicus (Rat).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae;
OC Murinae; Rattus.
OX NCBI_TaxID=10116;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA], PARTIAL PROTEIN SEQUENCE, AND ACETYLATION AT
RP SER-2.
RC TISSUE=Liver;
RX PubMed=8530410; DOI=10.1074/jbc.270.50.30060;
RA Oka T., Tsuji H., Noda C., Sakai K., Hong Y.-M., Suzuki I., Munoz S.,
RA Natori Y.;
RT "Isolation and characterization of a novel perchloric acid-soluble protein
RT inhibiting cell-free protein synthesis.";
RL J. Biol. Chem. 270:30060-30067(1995).
RN [2]
RP NUCLEOTIDE SEQUENCE [MRNA], AND TISSUE SPECIFICITY.
RC TISSUE=Kidney, and Liver;
RX PubMed=8385007; DOI=10.1111/j.1432-1033.1993.tb17704.x;
RA Levy-Favatier F., Cuisset L., Nedelec B., Tichonicky L., Kruh J.,
RA Delpech M.;
RT "Characterization, purification and cDNA cloning of a rat perchloric-acid-
RT soluble 23-kDa protein present only in liver and kidney.";
RL Eur. J. Biochem. 212:665-673(1993).
RN [3]
RP NUCLEOTIDE SEQUENCE [MRNA].
RC STRAIN=Dahl salt-sensitive;
RA Lighthall G., Hamlyn J.M.;
RL Submitted (JUL-1997) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC TISSUE=Kidney;
RX PubMed=15489334; DOI=10.1101/gr.2596504;
RG The MGC Project Team;
RT "The status, quality, and expansion of the NIH full-length cDNA project:
RT the Mammalian Gene Collection (MGC).";
RL Genome Res. 14:2121-2127(2004).
RN [5]
RP PROTEIN SEQUENCE OF 14-29 AND 79-97, AND IDENTIFICATION BY MASS
RP SPECTROMETRY.
RC STRAIN=Sprague-Dawley; TISSUE=Spinal cord;
RA Lubec G., Afjehi-Sadat L.;
RL Submitted (NOV-2006) to UniProtKB.
RN [6]
RP SUBCELLULAR LOCATION.
RX PubMed=11003673; DOI=10.1128/mcb.20.20.7784-7797.2000;
RA Oxelmark E., Marchini A., Malanchi I., Magherini F., Jaquet L.,
RA Hajibagheri M.A., Blight K.J., Jauniaux J.-C., Tommasino M.;
RT "Mmf1p, a novel yeast mitochondrial protein conserved throughout evolution
RT and involved in maintenance of the mitochondrial genome.";
RL Mol. Cell. Biol. 20:7784-7797(2000).
RN [7]
RP FUNCTION, AND CATALYTIC ACTIVITY.
RX PubMed=10400702; DOI=10.1074/jbc.274.29.20688;
RA Morishita R., Kawagoshi A., Sawasaki T., Madin K., Ogasawara T., Oka T.,
RA Endo Y.;
RT "Ribonuclease activity of rat liver perchloric acid-soluble protein, a
RT potent inhibitor of protein synthesis.";
RL J. Biol. Chem. 274:20688-20692(1999).
RN [8]
RP SUBCELLULAR LOCATION.
RC TISSUE=Liver;
RX PubMed=17416349; DOI=10.1016/j.bbrc.2007.03.136;
RA Antonenkov V.D., Ohlmeier S., Sormunen R.T., Hiltunen J.K.;
RT "UK114, a YjgF/Yer057p/UK114 family protein highly conserved from bacteria
RT to mammals, is localized in rat liver peroxisomes.";
RL Biochem. Biophys. Res. Commun. 357:252-257(2007).
RN [9]
RP X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS) OF 2-137.
RA Djinovic Carugo K., Oka T.;
RT "Crystal structure of perchloric acid soluble protein-a translational
RT inhibitor.";
RL Submitted (MAR-1999) to the PDB data bank.
CC -!- FUNCTION: Catalyzes the hydrolytic deamination of enamine/imine
CC intermediates that form during the course of normal metabolism. May
CC facilitate the release of ammonia from these potentially toxic reactive
CC metabolites, reducing their impact on cellular components. It may act
CC on enamine/imine intermediates formed by several types of pyridoxal-5'-
CC phosphate-dependent dehydratases including L-threonine dehydratase.
CC {ECO:0000250|UniProtKB:P52758}.
CC -!- FUNCTION: Also promotes endoribonucleolytic cleavage of some
CC transcripts by promoting recruitment of the ribonuclease P/MRP complex
CC (PubMed:10400702). Acts by bridging YTHDF2 and the ribonuclease P/MRP
CC complex (By similarity). RIDA/HRSP12 binds to N6-methyladenosine (m6A)-
CC containing mRNAs containing a 5'-GGUUC-3' motif: cooperative binding of
CC RIDA/HRSP12 and YTHDF2 to such transcripts lead to recruitment of the
CC ribonuclease P/MRP complex and subsequent endoribonucleolytic cleavage
CC (By similarity). {ECO:0000250|UniProtKB:P52758,
CC ECO:0000269|PubMed:10400702}.
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:0000250|UniProtKB:P52758};
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 Evidence={ECO:0000250|UniProtKB:P52758};
CC -!- SUBUNIT: Homotrimer. Interacts with YTHDF2.
CC {ECO:0000250|UniProtKB:P52758}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250|UniProtKB:P52758}. Nucleus
CC {ECO:0000250|UniProtKB:P52758}. Peroxisome
CC {ECO:0000269|PubMed:11003673}. Mitochondrion
CC {ECO:0000269|PubMed:17416349}. Note=Mostly cytoplasmic but, in less
CC differentiated cells occasionally nuclear.
CC {ECO:0000250|UniProtKB:P52758}.
CC -!- TISSUE SPECIFICITY: Liver and kidney. {ECO:0000269|PubMed:8385007}.
CC -!- SIMILARITY: Belongs to the RutC family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=CAB36976.1; Type=Frameshift; Evidence={ECO:0000305};
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DR EMBL; D49363; BAA08359.1; -; mRNA.
DR EMBL; X70825; CAB36976.1; ALT_FRAME; mRNA.
DR EMBL; AF015949; AAB70815.1; -; mRNA.
DR EMBL; BC078779; AAH78779.1; -; mRNA.
DR PIR; S30349; S30349.
DR RefSeq; NP_113902.1; NM_031714.1.
DR PDB; 1QAH; X-ray; 1.80 A; A/B=2-137.
DR PDBsum; 1QAH; -.
DR AlphaFoldDB; P52759; -.
DR SMR; P52759; -.
DR STRING; 10116.ENSRNOP00000007430; -.
DR iPTMnet; P52759; -.
DR PhosphoSitePlus; P52759; -.
DR PaxDb; P52759; -.
DR PRIDE; P52759; -.
DR GeneID; 65151; -.
DR KEGG; rno:65151; -.
DR UCSC; RGD:70940; rat.
DR CTD; 10247; -.
DR RGD; 70940; Rida.
DR VEuPathDB; HostDB:ENSRNOG00000005437; -.
DR eggNOG; KOG2317; Eukaryota.
DR HOGENOM; CLU_100715_7_1_1; -.
DR InParanoid; P52759; -.
DR OMA; GSYFKEP; -.
DR OrthoDB; 1435276at2759; -.
DR PhylomeDB; P52759; -.
DR Reactome; R-RNO-8849175; Threonine catabolism.
DR EvolutionaryTrace; P52759; -.
DR PRO; PR:P52759; -.
DR Proteomes; UP000002494; Chromosome 7.
DR Bgee; ENSRNOG00000005437; Expressed in kidney and 20 other tissues.
DR Genevisible; P52759; RN.
DR GO; GO:0005737; C:cytoplasm; ISO:RGD.
DR GO; GO:0005829; C:cytosol; IDA:RGD.
DR GO; GO:0005759; C:mitochondrial matrix; IDA:UniProtKB.
DR GO; GO:0005739; C:mitochondrion; IBA:GO_Central.
DR GO; GO:0005634; C:nucleus; IDA:RGD.
DR GO; GO:0005777; C:peroxisome; IDA:RGD.
DR GO; GO:0120242; F:2-iminobutanoate deaminase activity; ISS: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:0016892; F:endoribonuclease activity, producing 3'-phosphomonoesters; IDA:RGD.
DR GO; GO:0042802; F:identical protein binding; IPI:RGD.
DR GO; GO:0043167; F:ion binding; IDA:RGD.
DR GO; GO:0036041; F:long-chain fatty acid binding; IDA:RGD.
DR GO; GO:0003729; F:mRNA binding; ISS:UniProtKB.
DR GO; GO:0046914; F:transition metal ion binding; IDA:RGD.
DR GO; GO:0007420; P:brain development; IEP:RGD.
DR GO; GO:0070314; P:G1 to G0 transition; IEP:RGD.
DR GO; GO:0001822; P:kidney development; IEP:RGD.
DR GO; GO:0006629; P:lipid metabolic process; IEA:UniProtKB-KW.
DR GO; GO:0030324; P:lung development; IEP:RGD.
DR GO; GO:0006402; P:mRNA catabolic process; ISS:UniProtKB.
DR GO; GO:0061157; P:mRNA destabilization; ISS:UniProtKB.
DR GO; GO:0050680; P:negative regulation of epithelial cell proliferation; IMP:RGD.
DR GO; GO:0017148; P:negative regulation of translation; IDA:RGD.
DR GO; GO:1901565; P:organonitrogen compound catabolic process; ISS:UniProtKB.
DR GO; GO:0033993; P:response to lipid; IEP:RGD.
DR GO; GO:1902074; P:response to salt; IEP:RGD.
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; Acetylation; Cytoplasm; Direct protein sequencing; Hydrolase;
KW Lipid metabolism; Mitochondrion; Nucleus; Peroxisome; Phosphoprotein;
KW Reference proteome; RNA-binding.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:8530410"
FT CHAIN 2..137
FT /note="2-iminobutanoate/2-iminopropanoate deaminase"
FT /id="PRO_0000170310"
FT MOD_RES 2
FT /note="N-acetylserine"
FT /evidence="ECO:0000269|PubMed:8530410"
FT MOD_RES 13
FT /note="N6-succinyllysine"
FT /evidence="ECO:0000250|UniProtKB:P52760"
FT MOD_RES 60
FT /note="N6-succinyllysine"
FT /evidence="ECO:0000250|UniProtKB:P52760"
FT MOD_RES 67
FT /note="N6-succinyllysine"
FT /evidence="ECO:0000250|UniProtKB:P52760"
FT MOD_RES 74
FT /note="Phosphothreonine"
FT /evidence="ECO:0000250|UniProtKB:P52758"
FT CONFLICT 56
FT /note="K -> N (in Ref. 3; AAB70815)"
FT /evidence="ECO:0000305"
FT CONFLICT 137
FT /note="L -> V (in Ref. 2; CAB36976)"
FT /evidence="ECO:0000305"
FT STRAND 6..9
FT /evidence="ECO:0007829|PDB:1QAH"
FT STRAND 18..20
FT /evidence="ECO:0007829|PDB:1QAH"
FT STRAND 23..27
FT /evidence="ECO:0007829|PDB:1QAH"
FT STRAND 30..36
FT /evidence="ECO:0007829|PDB:1QAH"
FT TURN 41..43
FT /evidence="ECO:0007829|PDB:1QAH"
FT HELIX 51..68
FT /evidence="ECO:0007829|PDB:1QAH"
FT HELIX 73..75
FT /evidence="ECO:0007829|PDB:1QAH"
FT STRAND 76..84
FT /evidence="ECO:0007829|PDB:1QAH"
FT HELIX 86..88
FT /evidence="ECO:0007829|PDB:1QAH"
FT HELIX 89..97
FT /evidence="ECO:0007829|PDB:1QAH"
FT STRAND 106..111
FT /evidence="ECO:0007829|PDB:1QAH"
FT HELIX 116..118
FT /evidence="ECO:0007829|PDB:1QAH"
FT STRAND 120..128
FT /evidence="ECO:0007829|PDB:1QAH"
SQ SEQUENCE 137 AA; 14303 MW; F521725AA4324970 CRC64;
MSSIIRKVIS TSKAPAAIGA YSQAVLVDRT IYVSGQIGMD PSSGQLVPGG VAEEAKQALK
NLGEILKAAG CDFTNVVKTT VLLADINDFG TVNEIYKTYF QGNLPARAAY QVAALPKGSR
IEIEAIAVQG PFTTAGL
