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   24-JAN-2024, entry version 136.
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.Q945K7; -.
DR   PaxDb; 3702-AT5G03290-1; -.
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; AT5G03290; IDH-V.
DR   eggNOG; KOG0785; Eukaryota.
DR   HOGENOM; CLU_031953_0_1_1; -.
DR   InParanoid; Q945K7; -.
DR   OMA; CVRPCRY; -.
DR   OrthoDB; 143577at2759; -.
DR   PhylomeDB; Q945K7; -.
DR   BioCyc; MetaCyc:AT5G03290-MONOMER; -.
DR   BRENDA; 1.1.1.41; 399.
DR   PRO; PR:Q945K7; -.
DR   Proteomes; UP000006548; Chromosome 5.
DR   ExpressionAtlas; Q945K7; baseline and differential.
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; TAS:TAIR.
DR   Gene3D; 3.40.718.10; Isopropylmalate Dehydrogenase; 1.
DR   InterPro; IPR019818; IsoCit/isopropylmalate_DH_CS.
DR   InterPro; IPR004434; Isocitrate_DH_NAD.
DR   InterPro; IPR024084; IsoPropMal-DH-like_dom.
DR   NCBIfam; TIGR00175; mito_nad_idh; 1.
DR   PANTHER; PTHR11835; DECARBOXYLATING DEHYDROGENASES-ISOCITRATE, ISOPROPYLMALATE, TARTRATE; 1.
DR   PANTHER; PTHR11835:SF34; ISOCITRATE DEHYDROGENASE [NAD] SUBUNIT ALPHA, MITOCHONDRIAL; 1.
DR   Pfam; PF00180; Iso_dh; 1.
DR   SMART; SM01329; Iso_dh; 1.
DR   SUPFAM; SSF53659; Isocitrate/Isopropylmalate dehydrogenase-like; 1.
DR   PROSITE; PS00470; IDH_IMDH; 1.
DR   Genevisible; Q945K7; AT.
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
//