MDHM1_ARATH
ID MDHM1_ARATH Reviewed; 341 AA.
AC Q9ZP06; Q8LBB9; Q9MAH7;
DT 01-DEC-2000, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-1999, sequence version 1.
DT 03-AUG-2022, entry version 182.
DE RecName: Full=Malate dehydrogenase 1, mitochondrial {ECO:0000305};
DE EC=1.1.1.37 {ECO:0000269|PubMed:26203119};
DE AltName: Full=Mitochondrial MDH1 {ECO:0000303|PubMed:20876337};
DE Short=mMDH1 {ECO:0000303|PubMed:20876337};
DE AltName: Full=Mitochondrial NAD-dependent malate dehydrogenase 1 {ECO:0000305};
DE Short=mNAD-MDH 1 {ECO:0000305};
DE Short=mtNAD-MDH1 {ECO:0000303|PubMed:20876337};
DE Flags: Precursor;
GN OrderedLocusNames=At1g53240; ORFNames=F12M16.14;
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 [MRNA].
RC STRAIN=cv. Columbia;
RX PubMed=9774405; DOI=10.1074/jbc.273.43.27927;
RA Berkemeyer M., Scheibe R., Ocheretina O.;
RT "A novel, non-redox-regulated NAD-dependent malate dehydrogenase from
RT chloroplasts of Arabidopsis thaliana L.";
RL J. Biol. Chem. 273:27927-27933(1998).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130712; DOI=10.1038/35048500;
RA Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O.,
RA Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E.,
RA Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K., Conn L.,
RA Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P.,
RA Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D.,
RA Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J.,
RA Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L.,
RA Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A.,
RA Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A.,
RA Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M.,
RA Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M.,
RA Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P.,
RA Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D.,
RA Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D.,
RA Yu G., Fraser C.M., Venter J.C., Davis R.W.;
RT "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana.";
RL Nature 408:816-820(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 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 [6]
RP PROTEIN SEQUENCE OF 23-37, AND SUBCELLULAR LOCATION.
RC TISSUE=Leaf, and Stem;
RX PubMed=11743114; DOI=10.1104/pp.010474;
RA Kruft V., Eubel H., Jaensch L., Werhahn W., Braun H.-P.;
RT "Proteomic approach to identify novel mitochondrial proteins in
RT Arabidopsis.";
RL Plant Physiol. 127:1694-1710(2001).
RN [7]
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 [8]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=cv. Landsberg erecta;
RX PubMed=17272265; DOI=10.1074/mcp.m600408-mcp200;
RA Maor R., Jones A., Nuehse T.S., Studholme D.J., Peck S.C., Shirasu K.;
RT "Multidimensional protein identification technology (MudPIT) analysis of
RT ubiquitinated proteins in plants.";
RL Mol. Cell. Proteomics 6:601-610(2007).
RN [9]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=19376835; DOI=10.1104/pp.109.138677;
RA Reiland S., Messerli G., Baerenfaller K., Gerrits B., Endler A.,
RA Grossmann J., Gruissem W., Baginsky S.;
RT "Large-scale Arabidopsis phosphoproteome profiling reveals novel
RT chloroplast kinase substrates and phosphorylation networks.";
RL Plant Physiol. 150:889-903(2009).
RN [10]
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 [11]
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 [12]
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 [13]
RP ACTIVITY REGULATION, BIOPHYSICOCHEMICAL PROPERTIES, AND DISULFIDE BOND.
RX PubMed=26946085; DOI=10.1016/j.bbabio.2016.03.001;
RA Yoshida K., Hisabori T.;
RT "Adenine nucleotide-dependent and redox-independent control of
RT mitochondrial malate dehydrogenase activity in Arabidopsis thaliana.";
RL Biochim. Biophys. Acta 1857:810-818(2016).
RN [14]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=26889011; DOI=10.1093/jxb/erw030;
RA Linden P., Keech O., Stenlund H., Gardestroem P., Moritz T.;
RT "Reduced mitochondrial malate dehydrogenase activity has a strong effect on
RT photorespiratory metabolism as revealed by 13C labelling.";
RL J. Exp. Bot. 67:3123-3135(2016).
RN [15]
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). Its activity is essential to
CC shuttle reductants out from the mitochondria to support the
CC photorespiratory flux (PubMed:26889011). Can convert 2-oxoglutarate to
CC (S)-2-hydroxyglutarate in vitro (PubMed:26203119).
CC {ECO:0000269|PubMed:20876337, ECO:0000269|PubMed:26203119,
CC ECO:0000269|PubMed:26889011, ECO:0000269|PubMed:27208265,
CC 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 -!- ACTIVITY REGULATION: Negatively regulated by ATP. Not redox-regulated.
CC The formation of intramolecular disulfide bonds does not alter
CC enzymatic activity. {ECO:0000269|PubMed:26946085}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.8 mM for malate (at pH 7.5) {ECO:0000269|PubMed:26946085};
CC KM=0.11 mM for oxaloacetate (at pH 7.5)
CC {ECO:0000269|PubMed:26946085};
CC KM=0.27 mM for oxaloacetate (at pH 7.4)
CC {ECO:0000269|PubMed:26203119};
CC KM=0.6 mM for NAD(+) (at pH 7.5) {ECO:0000269|PubMed:26946085};
CC KM=0.23 mM for NADH (at pH 7.5) {ECO:0000269|PubMed:26946085};
CC KM=41 mM for 2-ketoglutarate (at pH 7.4)
CC {ECO:0000269|PubMed:26203119};
CC Vmax=0.087 mmol/min/mg enzyme toward malate (at pH 7.5)
CC {ECO:0000269|PubMed:26946085};
CC Vmax=0.03 mmol/min/mg enzyme toward malate (at pH 7.4)
CC {ECO:0000269|PubMed:26203119};
CC Vmax=1.2 mmol/min/mg enzyme toward oxaloacetate (at pH 7.5)
CC {ECO:0000269|PubMed:26946085};
CC Vmax=2.39 mmol/min/mg enzyme toward oxaloacetate (at pH 7.4)
CC {ECO:0000269|PubMed:26203119};
CC Vmax=79 umol/min/mg enzyme toward NAD(+) (at pH 7.5)
CC {ECO:0000269|PubMed:26946085};
CC Vmax=2732 umol/min/mg enzyme toward NADH (at pH 7.5)
CC {ECO:0000269|PubMed:26946085};
CC Vmax=0.38 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:11743114, ECO:0000269|PubMed:14671022,
CC ECO:0000305|PubMed:25732537}.
CC -!- TISSUE SPECIFICITY: Expressed in rosette leaves.
CC {ECO:0000269|PubMed:20876337}.
CC -!- PTM: Forms intramolecular disulfide bonds.
CC {ECO:0000269|PubMed:26946085}.
CC -!- DISRUPTION PHENOTYPE: Slight reduction of rosette leaf size and
CC reduction by 50 percents in fresh weight and seed production
CC (PubMed:26889011). The double mutant plants mmdh1 and mmdh2 have
CC decreased germination rate, grow slowly, are small, have increased
CC photorespiration and die before producing seeds (PubMed:20876337).
CC {ECO:0000269|PubMed:20876337, ECO:0000269|PubMed:26889011}.
CC -!- SIMILARITY: Belongs to the LDH/MDH superfamily. MDH type 1 family.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAF69549.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; AJ131205; CAA10320.1; -; mRNA.
DR EMBL; AC008007; AAF69549.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002684; AEE32910.1; -; Genomic_DNA.
DR EMBL; AF324670; AAG40021.1; -; mRNA.
DR EMBL; AF339684; AAK00366.1; -; mRNA.
DR EMBL; AY062580; AAL32658.1; -; mRNA.
DR EMBL; AY128783; AAM91183.1; -; mRNA.
DR EMBL; AY087304; AAM64855.1; -; mRNA.
DR PIR; T51311; T51311.
DR RefSeq; NP_564625.1; NM_104202.3.
DR AlphaFoldDB; Q9ZP06; -.
DR SMR; Q9ZP06; -.
DR BioGRID; 26982; 25.
DR IntAct; Q9ZP06; 1.
DR STRING; 3702.AT1G53240.1; -.
DR iPTMnet; Q9ZP06; -.
DR MetOSite; Q9ZP06; -.
DR SWISS-2DPAGE; Q9ZP06; -.
DR PaxDb; Q9ZP06; -.
DR PRIDE; Q9ZP06; -.
DR ProteomicsDB; 238769; -.
DR EnsemblPlants; AT1G53240.1; AT1G53240.1; AT1G53240.
DR GeneID; 841757; -.
DR Gramene; AT1G53240.1; AT1G53240.1; AT1G53240.
DR KEGG; ath:AT1G53240; -.
DR Araport; AT1G53240; -.
DR TAIR; locus:2009605; AT1G53240.
DR eggNOG; KOG1494; Eukaryota.
DR HOGENOM; CLU_047181_0_1_1; -.
DR InParanoid; Q9ZP06; -.
DR OMA; FRCMLVR; -.
DR OrthoDB; 976445at2759; -.
DR PhylomeDB; Q9ZP06; -.
DR BioCyc; ARA:AT1G53240-MON; -.
DR BioCyc; MetaCyc:AT1G53240-MON; -.
DR BRENDA; 1.1.1.37; 399.
DR PRO; PR:Q9ZP06; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; Q9ZP06; baseline and differential.
DR Genevisible; Q9ZP06; AT.
DR GO; GO:0009507; C:chloroplast; HDA:TAIR.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0005759; C:mitochondrial matrix; IEA:UniProtKB-SubCell.
DR GO; GO:0005739; C:mitochondrion; IDA:TAIR.
DR GO; GO:0005634; C:nucleus; HDA:TAIR.
DR GO; GO:0009505; C:plant-type cell wall; HDA:TAIR.
DR GO; GO:0005507; F:copper ion binding; HDA:TAIR.
DR GO; GO:0030060; F:L-malate dehydrogenase activity; IMP:TAIR.
DR GO; GO:0006108; P:malate metabolic process; IEA:InterPro.
DR GO; GO:0009409; P:response to cold; IEP:TAIR.
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 Direct protein sequencing; Disulfide bond; Mitochondrion; NAD;
KW Oxidoreductase; Reference proteome; Transit peptide;
KW Tricarboxylic acid cycle.
FT TRANSIT 1..22
FT /note="Mitochondrion"
FT /evidence="ECO:0000269|PubMed:11743114,
FT ECO:0000269|PubMed:25732537"
FT CHAIN 23..341
FT /note="Malate dehydrogenase 1, mitochondrial"
FT /id="PRO_0000018622"
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"
FT CONFLICT 17
FT /note="V -> A (in Ref. 5; AAM64855)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 341 AA; 35804 MW; D035C4C38785BE57 CRC64;
MFRSMLVRSS ASAKQAVIRR SFSSGSVPER KVAILGAAGG IGQPLALLMK LNPLVSSLSL
YDIANTPGVA ADVGHINTRS EVVGYMGDDN LAKALEGADL VIIPAGVPRK PGMTRDDLFN
INAGIVKNLC TAIAKYCPHA LINMISNPVN STVPIAAEIF KKAGMYDEKK LFGVTTLDVV
RARTFYAGKA NVPVAEVNVP VIGGHAGVTI LPLFSQATPQ ANLSSDILTA LTKRTQDGGT
EVVEAKAGKG SATLSMAYAG ALFADACLKG LNGVPDVIEC SYVQSTITEL PFFASKVRLG
KNGVEEVLDL GPLSDFEKEG LEALKPELKS SIEKGVKFAN Q
