MDHM2_ARATH
ID MDHM2_ARATH Reviewed; 341 AA.
AC Q9LKA3;
DT 21-FEB-2006, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2000, sequence version 1.
DT 03-AUG-2022, entry version 155.
DE RecName: Full=Malate dehydrogenase 2, mitochondrial {ECO:0000305};
DE EC=1.1.1.37 {ECO:0000269|PubMed:26203119};
DE AltName: Full=Mitochondrial MDH2 {ECO:0000303|PubMed:20876337};
DE Short=mMDH2 {ECO:0000303|PubMed:20876337};
DE AltName: Full=Mitochondrial NAD-dependent malate dehydrogenase 2 {ECO:0000305};
DE Short=mNAD-MDH 2 {ECO:0000305};
DE Short=mtNAD-MDH2 {ECO:0000303|PubMed:20876337};
DE Flags: Precursor;
GN OrderedLocusNames=At3g15020; ORFNames=K15M2.16;
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=10907853; DOI=10.1093/dnares/7.3.217;
RA Kaneko T., Katoh T., Sato S., Nakamura Y., Asamizu E., Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 3. II. Sequence
RT features of the 4,251,695 bp regions covered by 90 P1, TAC and BAC
RT clones.";
RL DNA Res. 7:217-221(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 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 [5]
RP IDENTIFICATION BY MASS SPECTROMETRY, FUNCTION, TISSUE SPECIFICITY, AND
RP DISRUPTION PHENOTYPE.
RX PubMed=20876337; DOI=10.1104/pp.110.161612;
RA Tomaz T., Bagard M., Pracharoenwattana I., Linden P., Lee C.P.,
RA Carroll A.J., Stroeher E., Smith S.M., Gardestroem P., Millar A.H.;
RT "Mitochondrial malate dehydrogenase lowers leaf respiration and alters
RT photorespiration and plant growth in Arabidopsis.";
RL Plant Physiol. 154:1143-1157(2010).
RN [6]
RP IDENTIFICATION BY MASS SPECTROMETRY, AND CLEAVAGE OF TRANSIT PEPTIDE AFTER
RP PHE-22.
RX PubMed=25732537; DOI=10.1093/jxb/erv064;
RA Carrie C., Venne A.S., Zahedi R.P., Soll J.;
RT "Identification of cleavage sites and substrate proteins for two
RT mitochondrial intermediate peptidases in Arabidopsis thaliana.";
RL J. Exp. Bot. 66:2691-2708(2015).
RN [7]
RP FUNCTION, CATALYTIC ACTIVITY, AND BIOPHYSICOCHEMICAL PROPERTIES.
RX PubMed=26203119; DOI=10.1093/pcp/pcv108;
RA Huedig M., Maier A., Scherrers I., Seidel L., Jansen E.E.,
RA Mettler-Altmann T., Engqvist M.K., Maurino V.G.;
RT "Plants possess a cyclic mitochondrial metabolic pathway similar to the
RT mammalian metabolic repair mechanism involving malate dehydrogenase and l-
RT 2-hydroxyglutarate dehydrogenase.";
RL Plant Cell Physiol. 56:1820-1830(2015).
RN [8]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=27208265; DOI=10.1104/pp.16.01654;
RA Sew Y.S., Stroeher E., Fenske R., Millar A.H.;
RT "Loss of mitochondrial malate dehydrogenase activity alters seed metabolism
RT impairing seed maturation and post-germination growth in Arabidopsis.";
RL Plant Physiol. 171:849-863(2016).
CC -!- FUNCTION: Catalyzes a reversible NAD-dependent dehydrogenase reaction
CC involved in central metabolism and redox homeostasis between organelle
CC compartments (Probable). Required for carbon dioxide and energy
CC partitioning in leaves. May limit photorespiration during the dark
CC phase (PubMed:20876337, PubMed:27208265). Can convert 2-ketoglutarate
CC to L-2-hydroxyglutarate in vitro (PubMed:26203119).
CC {ECO:0000269|PubMed:20876337, ECO:0000269|PubMed:26203119,
CC ECO:0000269|PubMed:27208265, ECO:0000305|PubMed:20876337}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(S)-malate + NAD(+) = H(+) + NADH + oxaloacetate;
CC Xref=Rhea:RHEA:21432, ChEBI:CHEBI:15378, ChEBI:CHEBI:15589,
CC ChEBI:CHEBI:16452, ChEBI:CHEBI:57540, ChEBI:CHEBI:57945; EC=1.1.1.37;
CC Evidence={ECO:0000269|PubMed:26203119};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=1.02 mM for oxaloacetate {ECO:0000269|PubMed:26203119};
CC KM=7 mM for 2-ketoglutarate {ECO:0000269|PubMed:26203119};
CC Vmax=0.67 mmol/min/mg enzyme toward oxaloacetate (at pH 7.4)
CC {ECO:0000269|PubMed:26203119};
CC Vmax=0.02 mmol/min/mg enzyme toward malate (at pH 7.4)
CC {ECO:0000269|PubMed:26203119};
CC Vmax=0.08 mmol/min/mg enzyme toward 2-ketoglutarate (at pH 7.4)
CC {ECO:0000269|PubMed:26203119};
CC -!- SUBUNIT: Homodimer. {ECO:0000250}.
CC -!- SUBCELLULAR LOCATION: Mitochondrion matrix
CC {ECO:0000269|PubMed:14671022, ECO:0000305|PubMed:25732537}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=1;
CC Comment=A number of isoforms are produced. According to EST
CC sequences.;
CC Name=1;
CC IsoId=Q9LKA3-1; Sequence=Displayed;
CC -!- TISSUE SPECIFICITY: Expressed in rosette leaves at low levels.
CC {ECO:0000269|PubMed:20876337}.
CC -!- DISRUPTION PHENOTYPE: No visible phenotype under normal growth
CC conditions, but the double mutant plants mmdh1 and mmdh2 have decreased
CC germination rate, grow slowly, are small, have increased
CC photorespiration and die before producing seeds.
CC {ECO:0000269|PubMed:20876337, ECO:0000269|PubMed:27208265}.
CC -!- SIMILARITY: Belongs to the LDH/MDH superfamily. MDH type 1 family.
CC {ECO:0000305}.
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DR EMBL; AP000370; BAA97065.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE75604.1; -; Genomic_DNA.
DR EMBL; AY045592; AAK73950.1; -; mRNA.
DR EMBL; AY093788; AAM10404.1; -; mRNA.
DR RefSeq; NP_188120.1; NM_112364.4. [Q9LKA3-1]
DR AlphaFoldDB; Q9LKA3; -.
DR SMR; Q9LKA3; -.
DR BioGRID; 6065; 26.
DR STRING; 3702.AT3G15020.1; -.
DR iPTMnet; Q9LKA3; -.
DR PaxDb; Q9LKA3; -.
DR PRIDE; Q9LKA3; -.
DR ProteomicsDB; 239048; -. [Q9LKA3-1]
DR EnsemblPlants; AT3G15020.1; AT3G15020.1; AT3G15020. [Q9LKA3-1]
DR GeneID; 820731; -.
DR Gramene; AT3G15020.1; AT3G15020.1; AT3G15020. [Q9LKA3-1]
DR KEGG; ath:AT3G15020; -.
DR Araport; AT3G15020; -.
DR TAIR; locus:2086340; AT3G15020.
DR eggNOG; KOG1494; Eukaryota.
DR HOGENOM; CLU_047181_0_2_1; -.
DR InParanoid; Q9LKA3; -.
DR OMA; VECTFVQ; -.
DR OrthoDB; 976445at2759; -.
DR PhylomeDB; Q9LKA3; -.
DR BRENDA; 1.1.1.37; 399.
DR PRO; PR:Q9LKA3; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q9LKA3; baseline and differential.
DR Genevisible; Q9LKA3; AT.
DR GO; GO:0048046; C:apoplast; HDA:TAIR.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0005829; C:cytosol; HDA:TAIR.
DR GO; GO:0005759; C:mitochondrial matrix; IEA:UniProtKB-SubCell.
DR GO; GO:0005739; C:mitochondrion; HDA:TAIR.
DR GO; GO:0005507; F:copper ion binding; HDA:TAIR.
DR GO; GO:0030060; F:L-malate dehydrogenase activity; IGI:TAIR.
DR GO; GO:0006108; P:malate metabolic process; IEA:InterPro.
DR GO; GO:0006099; P:tricarboxylic acid cycle; IEA:UniProtKB-KW.
DR CDD; cd01337; MDH_glyoxysomal_mitochondrial; 1.
DR Gene3D; 3.90.110.10; -; 1.
DR InterPro; IPR001557; L-lactate/malate_DH.
DR InterPro; IPR022383; Lactate/malate_DH_C.
DR InterPro; IPR001236; Lactate/malate_DH_N.
DR InterPro; IPR015955; Lactate_DH/Glyco_Ohase_4_C.
DR InterPro; IPR001252; Malate_DH_AS.
DR InterPro; IPR010097; Malate_DH_type1.
DR InterPro; IPR036291; NAD(P)-bd_dom_sf.
DR Pfam; PF02866; Ldh_1_C; 1.
DR Pfam; PF00056; Ldh_1_N; 1.
DR PIRSF; PIRSF000102; Lac_mal_DH; 1.
DR SUPFAM; SSF51735; SSF51735; 1.
DR SUPFAM; SSF56327; SSF56327; 1.
DR TIGRFAMs; TIGR01772; MDH_euk_gproteo; 1.
DR PROSITE; PS00068; MDH; 1.
PE 1: Evidence at protein level;
KW Alternative splicing; Mitochondrion; NAD; Oxidoreductase;
KW Reference proteome; Transit peptide; Tricarboxylic acid cycle.
FT TRANSIT 1..22
FT /note="Mitochondrion"
FT /evidence="ECO:0000269|PubMed:25732537"
FT CHAIN 23..341
FT /note="Malate dehydrogenase 2, mitochondrial"
FT /id="PRO_0000224148"
FT ACT_SITE 205
FT /note="Proton acceptor"
FT /evidence="ECO:0000250|UniProtKB:P11708"
FT BINDING 36..42
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250|UniProtKB:P40926"
FT BINDING 62
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250|UniProtKB:P40926"
FT BINDING 109
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P11708"
FT BINDING 115
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P11708"
FT BINDING 122
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250|UniProtKB:P40926"
FT BINDING 145..147
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250|UniProtKB:P40926"
FT BINDING 147
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P11708"
FT BINDING 181
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P11708"
FT BINDING 256
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250|UniProtKB:P40926"
SQ SEQUENCE 341 AA; 35875 MW; 38364CAE36712AE1 CRC64;
MFRSMIVRSA SPVKQGLLRR GFASESVPDR KVVILGAAGG IGQPLSLLMK LNPLVSSLSL
YDIANTPGVA ADVGHINTRS QVSGYMGDDD LGKALEGADL VIIPAGVPRK PGMTRDDLFN
INAGIVKNLS IAIAKYCPQA LVNMISNPVN STVPIAAEIF KKAGTYDEKK LFGVTTLDVV
RARTFYAGKS DVNVAEVNVP VVGGHAGITI LPLFSQASPQ ANLSDDLIRA LTKRTQDGGT
EVVEAKAGKG SATLSMAYAG ALFADACLKG LNGVPNVVEC SFVQSTITEL PFFASKVRLG
KNGVEEVLDL GPLSDFEKEG LEALKAELKS SIEKGIKFAN Q
