RIDA_ARATH
ID RIDA_ARATH Reviewed; 187 AA.
AC Q94JQ4; Q0WMP6; Q9LTQ3;
DT 29-OCT-2014, integrated into UniProtKB/Swiss-Prot.
DT 01-DEC-2001, sequence version 1.
DT 03-AUG-2022, entry version 133.
DE RecName: Full=Reactive Intermediate Deaminase A, chloroplastic {ECO:0000303|PubMed:25070638};
DE EC=3.5.99.10 {ECO:0000269|PubMed:25070638};
DE AltName: Full=2-iminobutanoate/2-iminopropanoate deaminase;
DE Flags: Precursor;
GN Name=RIDA {ECO:0000303|PubMed:25070638};
GN OrderedLocusNames=At3g20390 {ECO:0000312|Araport:AT3G20390};
GN ORFNames=MQC12.15 {ECO:0000303|PubMed:10819329};
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702 {ECO:0000312|EMBL:AAK53030.1};
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10819329; DOI=10.1093/dnares/7.2.131;
RA Sato S., Nakamura Y., Kaneko T., Katoh T., Asamizu E., Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 3. I. Sequence
RT features of the regions of 4,504,864 bp covered by sixty P1 and TAC
RT clones.";
RL DNA Res. 7:131-135(2000).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RA Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B.,
RA Feldmann K.A.;
RT "Full-length cDNA from Arabidopsis thaliana.";
RL Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RA Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A.,
RA Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y.,
RA Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.,
RA Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y.,
RA Shinozaki K.;
RT "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs.";
RL Submitted (JUL-2006) to the EMBL/GenBank/DDBJ databases.
RN [6]
RP FUNCTION, CATALYTIC ACTIVITY, MUTAGENESIS OF ARG-165, TISSUE SPECIFICITY,
RP SUBCELLULAR LOCATION, AND DISRUPTION PHENOTYPE.
RX PubMed=25070638; DOI=10.1105/tpc.114.126854;
RA Niehaus T.D., Nguyen T.N., Gidda S.K., ElBadawi-Sidhu M., Lambrecht J.A.,
RA McCarty D.R., Downs D.M., Cooper A.J., Fiehn O., Mullen R.T., Hanson A.D.;
RT "Arabidopsis and Maize RidA proteins preempt reactive enamine/imine damage
RT to branched-chain amino acid biosynthesis in plastids.";
RL Plant Cell 26:3010-3022(2014).
CC -!- FUNCTION: Hydrolyzes the Ser-derived enamine/imine product of Thr
CC dehydratase, protecting the plastidial branched-chain aminotransferase
CC BCAT3 (AC Q9M401) from inactivation. Involved in Ile biosynthesis.
CC {ECO:0000269|PubMed:25070638}.
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:25070638};
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:0000269|PubMed:25070638};
CC -!- PATHWAY: Amino-acid biosynthesis; L-isoleucine biosynthesis; 2-
CC oxobutanoate from L-threonine.
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast
CC {ECO:0000269|PubMed:25070638}.
CC -!- TISSUE SPECIFICITY: Expressed in leaves, petiols, petals, carpels and
CC shoot apex. {ECO:0000303|PubMed:25070638}.
CC -!- DISRUPTION PHENOTYPE: Reduced root growth and increased sensitivity of
CC the root to added Ser. {ECO:0000269|PubMed:25070638}.
CC -!- SIMILARITY: Belongs to the RutC family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAB02821.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=BAF01604.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
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DR EMBL; AB024036; BAB02821.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002686; AEE76372.1; -; Genomic_DNA.
DR EMBL; AF375446; AAK53030.1; -; mRNA.
DR EMBL; AY060547; AAL31178.1; -; mRNA.
DR EMBL; AY086036; AAM63246.1; -; mRNA.
DR EMBL; AK227774; BAE99756.1; -; mRNA.
DR EMBL; AK229768; BAF01604.1; ALT_INIT; mRNA.
DR RefSeq; NP_001327365.1; NM_001338478.1.
DR RefSeq; NP_188674.1; NM_112930.3.
DR PDB; 5HP7; X-ray; 2.00 A; A=68-187.
DR PDB; 5HP8; X-ray; 2.30 A; A/B/C=68-187.
DR PDBsum; 5HP7; -.
DR PDBsum; 5HP8; -.
DR AlphaFoldDB; Q94JQ4; -.
DR SMR; Q94JQ4; -.
DR BioGRID; 6916; 6.
DR IntAct; Q94JQ4; 1.
DR STRING; 3702.AT3G20390.1; -.
DR iPTMnet; Q94JQ4; -.
DR MetOSite; Q94JQ4; -.
DR PaxDb; Q94JQ4; -.
DR PRIDE; Q94JQ4; -.
DR EnsemblPlants; AT3G20390.1; AT3G20390.1; AT3G20390.
DR GeneID; 821584; -.
DR Gramene; AT3G20390.1; AT3G20390.1; AT3G20390.
DR KEGG; ath:AT3G20390; -.
DR Araport; AT3G20390; -.
DR TAIR; locus:2092374; AT3G20390.
DR eggNOG; KOG2317; Eukaryota.
DR HOGENOM; CLU_100715_0_0_1; -.
DR InParanoid; Q94JQ4; -.
DR OrthoDB; 1435276at2759; -.
DR PhylomeDB; Q94JQ4; -.
DR BRENDA; 3.5.99.10; 399.
DR PRO; PR:Q94JQ4; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q94JQ4; baseline and differential.
DR Genevisible; Q94JQ4; AT.
DR GO; GO:0009507; C:chloroplast; IDA:TAIR.
DR GO; GO:0009941; C:chloroplast envelope; HDA:TAIR.
DR GO; GO:0009570; C:chloroplast stroma; HDA:TAIR.
DR GO; GO:0005829; C:cytosol; HDA:TAIR.
DR GO; GO:0005739; C:mitochondrion; IBA:GO_Central.
DR GO; GO:0000325; C:plant-type vacuole; HDA:TAIR.
DR GO; GO:0009536; C:plastid; HDA:TAIR.
DR GO; GO:0009579; C:thylakoid; HDA:TAIR.
DR GO; GO:0120242; F:2-iminobutanoate deaminase activity; IEA:RHEA.
DR GO; GO:0120243; F:2-iminopropanoate deaminase activity; IEA:RHEA.
DR GO; GO:0019239; F:deaminase activity; IDA:TAIR.
DR GO; GO:0009082; P:branched-chain amino acid biosynthetic process; IMP:TAIR.
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; Chloroplast; Detoxification;
KW Hydrolase; Isoleucine biosynthesis; Plastid; Reference proteome;
KW Transit peptide.
FT TRANSIT 1..58
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT CHAIN 59..187
FT /note="Reactive Intermediate Deaminase A, chloroplastic"
FT /id="PRO_0000430561"
FT BINDING 165
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q7CP78"
FT SITE 79
FT /note="Stabilizes the substrate"
FT /evidence="ECO:0000250|UniProtKB:Q7CP78"
FT SITE 180
FT /note="Important for catalytic activity at high pH"
FT /evidence="ECO:0000250|UniProtKB:Q7CP78"
FT MUTAGEN 165
FT /note="R->A: Loss of activity."
FT /evidence="ECO:0000269|PubMed:25070638"
FT STRAND 82..85
FT /evidence="ECO:0007829|PDB:5HP7"
FT STRAND 88..94
FT /evidence="ECO:0007829|PDB:5HP7"
FT TURN 99..101
FT /evidence="ECO:0007829|PDB:5HP7"
FT STRAND 103..105
FT /evidence="ECO:0007829|PDB:5HP7"
FT HELIX 109..126
FT /evidence="ECO:0007829|PDB:5HP7"
FT HELIX 131..133
FT /evidence="ECO:0007829|PDB:5HP7"
FT STRAND 134..142
FT /evidence="ECO:0007829|PDB:5HP7"
FT HELIX 144..146
FT /evidence="ECO:0007829|PDB:5HP7"
FT HELIX 147..157
FT /evidence="ECO:0007829|PDB:5HP7"
FT STRAND 164..169
FT /evidence="ECO:0007829|PDB:5HP7"
FT HELIX 174..176
FT /evidence="ECO:0007829|PDB:5HP7"
FT STRAND 178..186
FT /evidence="ECO:0007829|PDB:5HP7"
SQ SEQUENCE 187 AA; 19816 MW; 40C19BA9C8EF2F44 CRC64;
MTWSVFRSIN TPTLDLSTAL RSTRTPLVAA GVGCATFAGV SLFRMSSRSP PFASLSVSAS
SVKKEVVSTE KAPAALGPYS QAIKANNLVF LSGVLGLIPE TGKFVSESVE DQTEQVLKNM
GEILKASGAD YSSVVKTTIM LADLADFKTV NEIYAKYFPA PSPARSTYQV AALPLNAKIE
IECIATL
