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Malate dehydrogenase 1, mitochondrial (EC 1.1.1.37) (Mitochondrial MDH1) (mMDH1) (Mitochondrial NAD-dependent malate dehydrogenase 1) (mNAD-MDH 1) (mtNAD-MDH1)

 MDHM1_ARATH             Reviewed;         341 AA.
Q9ZP06; Q8LBB9; Q9MAH7;
01-DEC-2000, integrated into UniProtKB/Swiss-Prot.
01-MAY-1999, sequence version 1.
12-SEP-2018, entry version 162.
RecName: Full=Malate dehydrogenase 1, mitochondrial {ECO:0000305};
EC=1.1.1.37 {ECO:0000269|PubMed:26203119};
AltName: Full=Mitochondrial MDH1 {ECO:0000303|PubMed:20876337};
Short=mMDH1 {ECO:0000303|PubMed:20876337};
AltName: Full=Mitochondrial NAD-dependent malate dehydrogenase 1 {ECO:0000305};
Short=mNAD-MDH 1 {ECO:0000305};
Short=mtNAD-MDH1 {ECO:0000303|PubMed:20876337};
Flags: Precursor;
OrderedLocusNames=At1g53240; ORFNames=F12M16.14;
Arabidopsis thaliana (Mouse-ear cress).
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; eudicotyledons; Gunneridae;
Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae;
Arabidopsis.
NCBI_TaxID=3702;
[1]
NUCLEOTIDE SEQUENCE [MRNA].
STRAIN=cv. Columbia;
PubMed=9774405; DOI=10.1074/jbc.273.43.27927;
Berkemeyer M., Scheibe R., Ocheretina O.;
"A novel, non-redox-regulated NAD-dependent malate dehydrogenase from
chloroplasts of Arabidopsis thaliana L.";
J. Biol. Chem. 273:27927-27933(1998).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=cv. Columbia;
PubMed=11130712; DOI=10.1038/35048500;
Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S.,
White O., Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y.,
Buehler E., Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W.,
Chung M.K., Conn L., Conway A.B., Conway A.R., Creasy T.H., Dewar K.,
Dunn P., Etgu P., Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y.,
Gill J.E., Goldsmith A.D., Haas B., Hansen N.F., Hughes B., Huizar L.,
Hunter J.L., Jenkins J., Johnson-Hopson C., Khan S., Khaykin E.,
Kim C.J., Koo H.L., Kremenetskaia I., Kurtz D.B., Kwan A., Lam B.,
Langin-Hooper S., Lee A., Lee J.M., Lenz C.A., Li J.H., Li Y.-P.,
Lin X., Liu S.X., Liu Z.A., Luros J.S., Maiti R., Marziali A.,
Militscher J., Miranda M., Nguyen M., Nierman W.C., Osborne B.I.,
Pai G., Peterson J., Pham P.K., Rizzo M., Rooney T., Rowley D.,
Sakano H., Salzberg S.L., Schwartz J.R., Shinn P., Southwick A.M.,
Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D.,
Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M.,
Wu D., Yu G., Fraser C.M., Venter J.C., Davis R.W.;
"Sequence and analysis of chromosome 1 of the plant Arabidopsis
thaliana.";
Nature 408:816-820(2000).
[3]
GENOME REANNOTATION.
STRAIN=cv. Columbia;
PubMed=27862469; DOI=10.1111/tpj.13415;
Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
Town C.D.;
"Araport11: a complete reannotation of the Arabidopsis thaliana
reference genome.";
Plant J. 89:789-804(2017).
[4]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
STRAIN=cv. Columbia;
PubMed=14593172; DOI=10.1126/science.1088305;
Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J.,
Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F.,
Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G.,
Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J.,
Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y.,
Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P.,
Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F.,
Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M.,
Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J.,
Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T.,
Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y.,
Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R.;
"Empirical analysis of transcriptional activity in the Arabidopsis
genome.";
Science 302:842-846(2003).
[5]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B.,
Feldmann K.A.;
"Full-length cDNA from Arabidopsis thaliana.";
Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases.
[6]
PROTEIN SEQUENCE OF 23-37, AND SUBCELLULAR LOCATION.
TISSUE=Leaf, and Stem;
PubMed=11743114; DOI=10.1104/pp.127.4.1694;
Kruft V., Eubel H., Jaensch L., Werhahn W., Braun H.-P.;
"Proteomic approach to identify novel mitochondrial proteins in
Arabidopsis.";
Plant Physiol. 127:1694-1710(2001).
[7]
IDENTIFICATION BY MASS SPECTROMETRY, AND SUBCELLULAR LOCATION [LARGE
SCALE ANALYSIS].
STRAIN=cv. Landsberg erecta;
PubMed=14671022; DOI=10.1105/tpc.016055;
Heazlewood J.L., Tonti-Filippini J.S., Gout A.M., Day D.A., Whelan J.,
Millar A.H.;
"Experimental analysis of the Arabidopsis mitochondrial proteome
highlights signaling and regulatory components, provides assessment of
targeting prediction programs, and indicates plant-specific
mitochondrial proteins.";
Plant Cell 16:241-256(2004).
[8]
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
STRAIN=cv. Landsberg erecta;
PubMed=17272265; DOI=10.1074/mcp.M600408-MCP200;
Maor R., Jones A., Nuehse T.S., Studholme D.J., Peck S.C., Shirasu K.;
"Multidimensional protein identification technology (MudPIT) analysis
of ubiquitinated proteins in plants.";
Mol. Cell. Proteomics 6:601-610(2007).
[9]
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=19376835; DOI=10.1104/pp.109.138677;
Reiland S., Messerli G., Baerenfaller K., Gerrits B., Endler A.,
Grossmann J., Gruissem W., Baginsky S.;
"Large-scale Arabidopsis phosphoproteome profiling reveals novel
chloroplast kinase substrates and phosphorylation networks.";
Plant Physiol. 150:889-903(2009).
[10]
IDENTIFICATION BY MASS SPECTROMETRY, FUNCTION, TISSUE SPECIFICITY, AND
DISRUPTION PHENOTYPE.
PubMed=20876337; DOI=10.1104/pp.110.161612;
Tomaz T., Bagard M., Pracharoenwattana I., Linden P., Lee C.P.,
Carroll A.J., Stroeher E., Smith S.M., Gardestroem P., Millar A.H.;
"Mitochondrial malate dehydrogenase lowers leaf respiration and alters
photorespiration and plant growth in Arabidopsis.";
Plant Physiol. 154:1143-1157(2010).
[11]
IDENTIFICATION BY MASS SPECTROMETRY, AND CLEAVAGE OF TRANSIT PEPTIDE
AFTER PHE-22.
PubMed=25732537; DOI=10.1093/jxb/erv064;
Carrie C., Venne A.S., Zahedi R.P., Soll J.;
"Identification of cleavage sites and substrate proteins for two
mitochondrial intermediate peptidases in Arabidopsis thaliana.";
J. Exp. Bot. 66:2691-2708(2015).
[12]
FUNCTION, CATALYTIC ACTIVITY, AND BIOPHYSICOCHEMICAL PROPERTIES.
PubMed=26203119; DOI=10.1093/pcp/pcv108;
Huedig M., Maier A., Scherrers I., Seidel L., Jansen E.E.,
Mettler-Altmann T., Engqvist M.K., Maurino V.G.;
"Plants possess a cyclic mitochondrial metabolic pathway similar to
the mammalian metabolic repair mechanism involving malate
dehydrogenase and l-2-hydroxyglutarate dehydrogenase.";
Plant Cell Physiol. 56:1820-1830(2015).
[13]
ACTIVITY REGULATION, BIOPHYSICOCHEMICAL PROPERTIES, AND DISULFIDE
BOND.
PubMed=26946085; DOI=10.1016/j.bbabio.2016.03.001;
Yoshida K., Hisabori T.;
"Adenine nucleotide-dependent and redox-independent control of
mitochondrial malate dehydrogenase activity in Arabidopsis thaliana.";
Biochim. Biophys. Acta 1857:810-818(2016).
[14]
FUNCTION, AND DISRUPTION PHENOTYPE.
PubMed=26889011; DOI=10.1093/jxb/erw030;
Linden P., Keech O., Stenlund H., Gardestroem P., Moritz T.;
"Reduced mitochondrial malate dehydrogenase activity has a strong
effect on photorespiratory metabolism as revealed by 13C labelling.";
J. Exp. Bot. 67:3123-3135(2016).
[15]
FUNCTION, AND DISRUPTION PHENOTYPE.
PubMed=27208265; DOI=10.1104/pp.16.01654;
Sew Y.S., Stroeher E., Fenske R., Millar A.H.;
"Loss of mitochondrial malate dehydrogenase activity alters seed
metabolism impairing seed maturation and post-germination growth in
Arabidopsis.";
Plant Physiol. 171:849-863(2016).
-!- FUNCTION: Catalyzes a reversible NAD-dependent dehydrogenase
reaction involved in central metabolism and redox homeostasis
between organelle compartments (Probable). Required for carbon
dioxide and energy partitioning in leaves. May limit
photorespiration during the dark phase (PubMed:20876337,
PubMed:27208265). Its activity is essential to shuttle reductants
out from the mitochondria to support the photorespiratory flux
(PubMed:26889011). Can convert 2-oxoglutarate to (S)-2-
hydroxyglutarate in vitro (PubMed:26203119).
{ECO:0000269|PubMed:20876337, ECO:0000269|PubMed:26203119,
ECO:0000269|PubMed:26889011, ECO:0000269|PubMed:27208265,
ECO:0000305|PubMed:20876337}.
-!- CATALYTIC ACTIVITY: (S)-malate + NAD(+) = oxaloacetate + NADH.
{ECO:0000269|PubMed:26203119}.
-!- ACTIVITY REGULATION: Negatively regulated by ATP. Not redox-
regulated. The formation of intramolecular disulfide bonds does
not alter enzymatic activity. {ECO:0000269|PubMed:26946085}.
-!- BIOPHYSICOCHEMICAL PROPERTIES:
Kinetic parameters:
KM=0.8 mM for malate (at pH 7.5) {ECO:0000269|PubMed:26946085};
KM=0.11 mM for oxaloacetate (at pH 7.5)
{ECO:0000269|PubMed:26946085};
KM=0.27 mM for oxaloacetate (at pH 7.4)
{ECO:0000269|PubMed:26203119};
KM=0.6 mM for NAD(+) (at pH 7.5) {ECO:0000269|PubMed:26946085};
KM=0.23 mM for NADH (at pH 7.5) {ECO:0000269|PubMed:26946085};
KM=41 mM for 2-ketoglutarate (at pH 7.4)
{ECO:0000269|PubMed:26203119};
Vmax=0.087 mmol/min/mg enzyme toward malate (at pH 7.5)
{ECO:0000269|PubMed:26946085};
Vmax=0.03 mmol/min/mg enzyme toward malate (at pH 7.4)
{ECO:0000269|PubMed:26203119};
Vmax=1.2 mmol/min/mg enzyme toward oxaloacetate (at pH 7.5)
{ECO:0000269|PubMed:26946085};
Vmax=2.39 mmol/min/mg enzyme toward oxaloacetate (at pH 7.4)
{ECO:0000269|PubMed:26203119};
Vmax=79 umol/min/mg enzyme toward NAD(+) (at pH 7.5)
{ECO:0000269|PubMed:26946085};
Vmax=2732 umol/min/mg enzyme toward NADH (at pH 7.5)
{ECO:0000269|PubMed:26946085};
Vmax=0.38 mmol/min/mg enzyme toward 2-ketoglutarate (at pH 7.4)
{ECO:0000269|PubMed:26203119};
-!- SUBUNIT: Homodimer. {ECO:0000250}.
-!- SUBCELLULAR LOCATION: Mitochondrion matrix
{ECO:0000269|PubMed:11743114, ECO:0000269|PubMed:14671022,
ECO:0000305|PubMed:25732537}.
-!- TISSUE SPECIFICITY: Expressed in rosette leaves.
{ECO:0000269|PubMed:20876337}.
-!- PTM: Forms intramolecular disulfide bonds.
{ECO:0000269|PubMed:26946085}.
-!- DISRUPTION PHENOTYPE: Slight reduction of rosette leaf size and
reduction by 50 percents in fresh weight and seed production
(PubMed:26889011). The double mutant plants mmdh1 and mmdh2 have
decreased germination rate, grow slowly, are small, have increased
photorespiration and die before producing seeds (PubMed:20876337).
{ECO:0000269|PubMed:20876337, ECO:0000269|PubMed:26889011}.
-!- SIMILARITY: Belongs to the LDH/MDH superfamily. MDH type 1 family.
{ECO:0000305}.
-!- SEQUENCE CAUTION:
Sequence=AAF69549.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
-----------------------------------------------------------------------
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Distributed under the Creative Commons Attribution (CC BY 4.0) License
-----------------------------------------------------------------------
EMBL; AJ131205; CAA10320.1; -; mRNA.
EMBL; AC008007; AAF69549.1; ALT_SEQ; Genomic_DNA.
EMBL; CP002684; AEE32910.1; -; Genomic_DNA.
EMBL; AF324670; AAG40021.1; -; mRNA.
EMBL; AF339684; AAK00366.1; -; mRNA.
EMBL; AY062580; AAL32658.1; -; mRNA.
EMBL; AY128783; AAM91183.1; -; mRNA.
EMBL; AY087304; AAM64855.1; -; mRNA.
PIR; T51311; T51311.
RefSeq; NP_564625.1; NM_104202.3.
UniGene; At.23771; -.
ProteinModelPortal; Q9ZP06; -.
SMR; Q9ZP06; -.
BioGrid; 26982; 2.
IntAct; Q9ZP06; 1.
STRING; 3702.AT1G53240.1; -.
iPTMnet; Q9ZP06; -.
SWISS-2DPAGE; Q9ZP06; -.
PaxDb; Q9ZP06; -.
PRIDE; Q9ZP06; -.
EnsemblPlants; AT1G53240.1; AT1G53240.1; AT1G53240.
GeneID; 841757; -.
Gramene; AT1G53240.1; AT1G53240.1; AT1G53240.
KEGG; ath:AT1G53240; -.
Araport; AT1G53240; -.
TAIR; locus:2009605; AT1G53240.
eggNOG; KOG1494; Eukaryota.
eggNOG; COG0039; LUCA.
HOGENOM; HOG000213792; -.
InParanoid; Q9ZP06; -.
KO; K00026; -.
OMA; CTFLNLD; -.
OrthoDB; EOG09360H2H; -.
PhylomeDB; Q9ZP06; -.
BioCyc; ARA:AT1G53240-MONOMER; -.
BioCyc; MetaCyc:AT1G53240-MONOMER; -.
BRENDA; 1.1.1.37; 399.
Reactome; R-ATH-70263; Gluconeogenesis.
Reactome; R-ATH-71403; Citric acid cycle (TCA cycle).
PRO; PR:Q9ZP06; -.
Proteomes; UP000006548; Chromosome 1.
ExpressionAtlas; Q9ZP06; baseline and differential.
Genevisible; Q9ZP06; AT.
GO; GO:0048046; C:apoplast; IDA:TAIR.
GO; GO:0005618; C:cell wall; IDA:TAIR.
GO; GO:0009507; C:chloroplast; IDA:TAIR.
GO; GO:0005759; C:mitochondrial matrix; IEA:UniProtKB-SubCell.
GO; GO:0005739; C:mitochondrion; IDA:TAIR.
GO; GO:0005507; F:copper ion binding; IDA:TAIR.
GO; GO:0030060; F:L-malate dehydrogenase activity; IMP:TAIR.
GO; GO:0005975; P:carbohydrate metabolic process; IEA:InterPro.
GO; GO:0042742; P:defense response to bacterium; IEP:TAIR.
GO; GO:0006108; P:malate metabolic process; IEA:InterPro.
GO; GO:0046686; P:response to cadmium ion; IEP:TAIR.
GO; GO:0009409; P:response to cold; IEP:TAIR.
GO; GO:0009651; P:response to salt stress; IEP:TAIR.
GO; GO:0006099; P:tricarboxylic acid cycle; IEA:UniProtKB-KW.
Gene3D; 3.90.110.10; -; 1.
InterPro; IPR001557; L-lactate/malate_DH.
InterPro; IPR022383; Lactate/malate_DH_C.
InterPro; IPR001236; Lactate/malate_DH_N.
InterPro; IPR015955; Lactate_DH/Glyco_Ohase_4_C.
InterPro; IPR001252; Malate_DH_AS.
InterPro; IPR010097; Malate_DH_type1.
InterPro; IPR036291; NAD(P)-bd_dom_sf.
Pfam; PF02866; Ldh_1_C; 1.
Pfam; PF00056; Ldh_1_N; 1.
PIRSF; PIRSF000102; Lac_mal_DH; 1.
SUPFAM; SSF51735; SSF51735; 1.
SUPFAM; SSF56327; SSF56327; 1.
TIGRFAMs; TIGR01772; MDH_euk_gproteo; 1.
PROSITE; PS00068; MDH; 1.
1: Evidence at protein level;
Complete proteome; Direct protein sequencing; Disulfide bond;
Mitochondrion; NAD; Oxidoreductase; Reference proteome;
Transit peptide; Tricarboxylic acid cycle.
TRANSIT 1 22 Mitochondrion.
{ECO:0000269|PubMed:11743114,
ECO:0000269|PubMed:25732537}.
CHAIN 23 341 Malate dehydrogenase 1, mitochondrial.
/FTId=PRO_0000018622.
NP_BIND 36 42 NAD. {ECO:0000250|UniProtKB:P40926}.
NP_BIND 145 147 NAD. {ECO:0000250|UniProtKB:P40926}.
ACT_SITE 205 205 Proton acceptor.
{ECO:0000250|UniProtKB:P11708}.
BINDING 62 62 NAD. {ECO:0000250|UniProtKB:P40926}.
BINDING 109 109 Substrate.
{ECO:0000250|UniProtKB:P11708}.
BINDING 115 115 Substrate.
{ECO:0000250|UniProtKB:P11708}.
BINDING 122 122 NAD. {ECO:0000250|UniProtKB:P40926}.
BINDING 147 147 Substrate.
{ECO:0000250|UniProtKB:P11708}.
BINDING 181 181 Substrate.
{ECO:0000250|UniProtKB:P11708}.
BINDING 256 256 NAD. {ECO:0000250|UniProtKB:P40926}.
CONFLICT 17 17 V -> A (in Ref. 5; AAM64855).
{ECO:0000305}.
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


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