IDH5_ARATH
ID IDH5_ARATH Reviewed; 374 AA.
AC Q945K7; Q9LZG1;
DT 09-JAN-2007, integrated into UniProtKB/Swiss-Prot.
DT 01-DEC-2001, sequence version 1.
DT 03-AUG-2022, entry version 131.
DE RecName: Full=Isocitrate dehydrogenase [NAD] catalytic subunit 5, mitochondrial;
DE EC=1.1.1.41 {ECO:0000305|PubMed:16527867};
DE AltName: Full=IDH-V;
DE AltName: Full=Isocitric dehydrogenase 5;
DE AltName: Full=NAD(+)-specific ICDH 5;
DE Flags: Precursor;
GN Name=IDH5; OrderedLocusNames=At5g03290; ORFNames=F12E4_20, MOK16.20;
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;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=9330910; DOI=10.1093/dnares/4.3.215;
RA Sato S., Kotani H., Nakamura Y., Kaneko T., Asamizu E., Fukami M.,
RA Miyajima N., Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 5. I. Sequence
RT features of the 1.6 Mb regions covered by twenty physically assigned P1
RT clones.";
RL DNA Res. 4:215-230(1997).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130714; DOI=10.1038/35048507;
RA Tabata S., Kaneko T., Nakamura Y., Kotani H., Kato T., Asamizu E.,
RA Miyajima N., Sasamoto S., Kimura T., Hosouchi T., Kawashima K., Kohara M.,
RA Matsumoto M., Matsuno A., Muraki A., Nakayama S., Nakazaki N., Naruo K.,
RA Okumura S., Shinpo S., Takeuchi C., Wada T., Watanabe A., Yamada M.,
RA Yasuda M., Sato S., de la Bastide M., Huang E., Spiegel L., Gnoj L.,
RA O'Shaughnessy A., Preston R., Habermann K., Murray J., Johnson D.,
RA Rohlfing T., Nelson J., Stoneking T., Pepin K., Spieth J., Sekhon M.,
RA Armstrong J., Becker M., Belter E., Cordum H., Cordes M., Courtney L.,
RA Courtney W., Dante M., Du H., Edwards J., Fryman J., Haakensen B.,
RA Lamar E., Latreille P., Leonard S., Meyer R., Mulvaney E., Ozersky P.,
RA Riley A., Strowmatt C., Wagner-McPherson C., Wollam A., Yoakum M., Bell M.,
RA Dedhia N., Parnell L., Shah R., Rodriguez M., Hoon See L., Vil D.,
RA Baker J., Kirchoff K., Toth K., King L., Bahret A., Miller B., Marra M.A.,
RA Martienssen R., McCombie W.R., Wilson R.K., Murphy G., Bancroft I.,
RA Volckaert G., Wambutt R., Duesterhoeft A., Stiekema W., Pohl T.,
RA Entian K.-D., Terryn N., Hartley N., Bent E., Johnson S., Langham S.-A.,
RA McCullagh B., Robben J., Grymonprez B., Zimmermann W., Ramsperger U.,
RA Wedler H., Balke K., Wedler E., Peters S., van Staveren M., Dirkse W.,
RA Mooijman P., Klein Lankhorst R., Weitzenegger T., Bothe G., Rose M.,
RA Hauf J., Berneiser S., Hempel S., Feldpausch M., Lamberth S.,
RA Villarroel R., Gielen J., Ardiles W., Bents O., Lemcke K., Kolesov G.,
RA Mayer K.F.X., Rudd S., Schoof H., Schueller C., Zaccaria P., Mewes H.-W.,
RA Bevan M., Fransz P.F.;
RT "Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana.";
RL Nature 408:823-826(2000).
RN [3]
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 [4]
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 [5]
RP IDENTIFICATION BY MASS SPECTROMETRY, AND SUBCELLULAR LOCATION [LARGE SCALE
RP ANALYSIS].
RC STRAIN=cv. Landsberg erecta;
RX PubMed=14671022; DOI=10.1105/tpc.016055;
RA Heazlewood J.L., Tonti-Filippini J.S., Gout A.M., Day D.A., Whelan J.,
RA Millar A.H.;
RT "Experimental analysis of the Arabidopsis mitochondrial proteome highlights
RT signaling and regulatory components, provides assessment of targeting
RT prediction programs, and indicates plant-specific mitochondrial proteins.";
RL Plant Cell 16:241-256(2004).
RN [6]
RP GENE FAMILY.
RX AGRICOLA=IND43633651; DOI=10.1016/j.plantsci.2003.12.012;
RA Lin M., Behal R.H., Oliver D.J.;
RT "Characterization of a mutation in the IDH-II subunit of the NAD(+)-
RT dependent isocitrate dehydrogenase from Arabidopsis thaliana.";
RL Plant Sci. 166:983-988(2004).
RN [7]
RP TISSUE SPECIFICITY, CATALYTIC ACTIVITY, AND SUBUNIT.
RX PubMed=16527867; DOI=10.1093/pcp/pcj030;
RA Lemaitre T., Hodges M.;
RT "Expression analysis of Arabidopsis thaliana NAD-dependent isocitrate
RT dehydrogenase genes shows the presence of a functional subunit that is
RT mainly expressed in the pollen and absent from vegetative organs.";
RL Plant Cell Physiol. 47:634-643(2006).
CC -!- FUNCTION: Performs an essential role in the oxidative function of the
CC citric acid cycle. {ECO:0000250|UniProtKB:P93032}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=D-threo-isocitrate + NAD(+) = 2-oxoglutarate + CO2 + NADH;
CC Xref=Rhea:RHEA:23632, ChEBI:CHEBI:15562, ChEBI:CHEBI:16526,
CC ChEBI:CHEBI:16810, ChEBI:CHEBI:57540, ChEBI:CHEBI:57945; EC=1.1.1.41;
CC Evidence={ECO:0000305|PubMed:16527867};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000250};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035; Evidence={ECO:0000250};
CC Note=Binds 1 Mg(2+) or Mn(2+) ion per subunit. {ECO:0000250};
CC -!- SUBUNIT: Heterooligomer of catalytic and regulatory subunits.
CC {ECO:0000305|PubMed:16527867}.
CC -!- SUBCELLULAR LOCATION: Mitochondrion {ECO:0000269|PubMed:14671022}.
CC -!- TISSUE SPECIFICITY: Ubiquitous. {ECO:0000269|PubMed:16527867}.
CC -!- SIMILARITY: Belongs to the isocitrate and isopropylmalate
CC dehydrogenases family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAB08389.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
CC Sequence=CAB83285.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
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DR EMBL; AB005240; BAB08389.1; ALT_INIT; Genomic_DNA.
DR EMBL; AL162751; CAB83285.1; ALT_INIT; Genomic_DNA.
DR EMBL; CP002688; AED90581.1; -; Genomic_DNA.
DR EMBL; AF412100; AAL06553.1; -; mRNA.
DR EMBL; AY099823; AAM20674.1; -; mRNA.
DR EMBL; BT008460; AAP37819.1; -; mRNA.
DR PIR; T48350; T48350.
DR RefSeq; NP_568113.1; NM_120407.6.
DR AlphaFoldDB; Q945K7; -.
DR SMR; Q945K7; -.
DR BioGRID; 17160; 3.
DR IntAct; Q945K7; 1.
DR STRING; 3702.AT5G03290.1; -.
DR PaxDb; Q945K7; -.
DR PRIDE; Q945K7; -.
DR ProteomicsDB; 248618; -.
DR EnsemblPlants; AT5G03290.1; AT5G03290.1; AT5G03290.
DR GeneID; 831884; -.
DR Gramene; AT5G03290.1; AT5G03290.1; AT5G03290.
DR KEGG; ath:AT5G03290; -.
DR Araport; AT5G03290; -.
DR TAIR; locus:2142604; AT5G03290.
DR eggNOG; KOG0785; Eukaryota.
DR HOGENOM; CLU_031953_0_1_1; -.
DR InParanoid; Q945K7; -.
DR OMA; CVRPCRY; -.
DR OrthoDB; 868374at2759; -.
DR PhylomeDB; Q945K7; -.
DR BioCyc; MetaCyc:AT5G03290-MON; -.
DR BRENDA; 1.1.1.41; 399.
DR PRO; PR:Q945K7; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q945K7; baseline and differential.
DR Genevisible; Q945K7; AT.
DR GO; GO:0005739; C:mitochondrion; HDA:TAIR.
DR GO; GO:0005886; C:plasma membrane; HDA:TAIR.
DR GO; GO:0005524; F:ATP binding; HDA:TAIR.
DR GO; GO:0004449; F:isocitrate dehydrogenase (NAD+) activity; IMP:TAIR.
DR GO; GO:0000287; F:magnesium ion binding; IEA:InterPro.
DR GO; GO:0051287; F:NAD binding; IEA:InterPro.
DR GO; GO:0008270; F:zinc ion binding; HDA:TAIR.
DR GO; GO:0006102; P:isocitrate metabolic process; IMP:TAIR.
DR GO; GO:0006099; P:tricarboxylic acid cycle; IBA:GO_Central.
DR InterPro; IPR019818; IsoCit/isopropylmalate_DH_CS.
DR InterPro; IPR004434; Isocitrate_DH_NAD.
DR InterPro; IPR024084; IsoPropMal-DH-like_dom.
DR Pfam; PF00180; Iso_dh; 1.
DR SMART; SM01329; Iso_dh; 1.
DR TIGRFAMs; TIGR00175; mito_nad_idh; 1.
DR PROSITE; PS00470; IDH_IMDH; 1.
PE 1: Evidence at protein level;
KW Magnesium; Manganese; Metal-binding; Mitochondrion; NAD; Oxidoreductase;
KW Reference proteome; Transit peptide; Tricarboxylic acid cycle.
FT TRANSIT 1..44
FT /note="Mitochondrion"
FT /evidence="ECO:0000255"
FT CHAIN 45..374
FT /note="Isocitrate dehydrogenase [NAD] catalytic subunit 5,
FT mitochondrial"
FT /id="PRO_0000271291"
FT BINDING 127
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 137
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 158
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 245
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250|UniProtKB:P50213"
FT BINDING 245
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 269
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250|UniProtKB:P50213"
FT BINDING 273
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250|UniProtKB:P50213"
FT SITE 165
FT /note="Critical for catalysis"
FT /evidence="ECO:0000250"
FT SITE 212
FT /note="Critical for catalysis"
FT /evidence="ECO:0000250"
SQ SEQUENCE 374 AA; 40625 MW; 723D0150C360F7A1 CRC64;
MTMAANLARR LIGNRSTQIL GAVNSSSGAA SSVARAFCSS TTPITATLFP GDGIGPEIAE
SVKKVFTTAG VPIEWEEHYV GTEIDPRTQS FLTWESLESV RRNKVGLKGP MATPIGKGHR
SLNLTLRKEL NLYANVRPCY SLPGYKTRYD DVDLITIREN TEGEYSGLEH QVVRGVVESL
KIITRQASLR VAEYAFLYAK THGRERVSAI HKANIMQKTD GLFLKCCREV AEKYPEITYE
EVVIDNCCMM LVKNPALFDV LVMPNLYGDI ISDLCAGLVG GLGLTPSCNI GEDGVALAEA
VHGSAPDIAG KNLANPTALL LSGVMMLRHL KFNEQAEQIH SAIINTIAEG KYRTADLGGS
STTTEFTKAI CDHL
