ID   MDHC1_ARATH             Reviewed;         332 AA.
AC   P93819;
DT   01-DEC-2000, integrated into UniProtKB/Swiss-Prot.
DT   01-JAN-1998, sequence version 2.
DT   27-MAR-2024, entry version 185.
DE   RecName: Full=Malate dehydrogenase 1, cytoplasmic {ECO:0000305};
DE            EC=1.1.1.37 {ECO:0000269|PubMed:29194485};
DE   AltName: Full=Cytosolic NAD-dependent malate dehydrogenase 1 {ECO:0000305};
DE            Short=cNAD-MDH1 {ECO:0000303|PubMed:20876337};
DE   AltName: Full=Cytosolic malate dehydrogenase 1 {ECO:0000303|PubMed:20876337};
DE            Short=Cytosolic MDH1 {ECO:0000305};
GN   Name=MDH1; OrderedLocusNames=At1g04410; ORFNames=F19P19.13;
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=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   [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   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   [5]
RP   UBIQUITINATION [LARGE SCALE ANALYSIS] AT LYS-119, AND IDENTIFICATION BY
RP   MASS SPECTROMETRY.
RX   PubMed=19292762; DOI=10.1111/j.1365-313x.2009.03862.x;
RA   Saracco S.A., Hansson M., Scalf M., Walker J.M., Smith L.M., Vierstra R.D.;
RT   "Tandem affinity purification and mass spectrometric analysis of
RT   ubiquitylated proteins in Arabidopsis.";
RL   Plant J. 59:344-358(2009).
RN   [6]
RP   FUNCTION, AND TISSUE SPECIFICITY.
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   [7]
RP   INTERACTION WITH GRF1; GRF3 AND GRF8.
RX   PubMed=22104211; DOI=10.1186/1752-0509-5-192;
RA   Diaz C., Kusano M., Sulpice R., Araki M., Redestig H., Saito K., Stitt M.,
RA   Shin R.;
RT   "Determining novel functions of Arabidopsis 14-3-3 proteins in central
RT   metabolic processes.";
RL   BMC Syst. Biol. 5:192-192(2011).
RN   [8]
RP   X-RAY CRYSTALLOGRAPHY (1.35 ANGSTROMS) IN COMPLEX WITH NAD AND
RP   OXALOACETATE, CATALYTIC ACTIVITY, ACTIVITY REGULATION, BIOPHYSICOCHEMICAL
RP   PROPERTIES, SUBUNIT, DISULFIDE BOND, INTERACTION WITH TRX1; TRX2; TRX3;
RP   TRX4 AND TRX5, AND OXIDATION AT MET-56 AND MET-97.
RX   PubMed=29194485; DOI=10.1093/jxb/erx396;
RA   Huang J., Niazi A.K., Young D., Rosado L.A., Vertommen D., Bodra N.,
RA   Abdelgawwad M.R., Vignols F., Wei B., Wahni K., Bashandy T., Bariat L.,
RA   Van Breusegem F., Messens J., Reichheld J.P.;
RT   "Self-protection of cytosolic malate dehydrogenase against oxidative stress
RT   in Arabidopsis.";
RL   J. Exp. Bot. 69:3491-3505(2018).
CC   -!- FUNCTION: Catalyzes a reversible NAD-dependent dehydrogenase reaction
CC       involved in central metabolism and redox homeostasis between organellar
CC       compartments. {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:0000255|PROSITE-ProRule:PRU10004,
CC         ECO:0000269|PubMed:29194485};
CC   -!- ACTIVITY REGULATION: Decreased activity upon treatment with hydrogen
CC       peroxide. {ECO:0000269|PubMed:29194485}.
CC   -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC       Kinetic parameters:
CC         KM=238 uM for oxaloacetate {ECO:0000269|PubMed:29194485};
CC         KM=72 uM for NADH {ECO:0000269|PubMed:29194485};
CC         Note=kcat is 608 sec(-1) with oxaloacetate as substrate
CC         (PubMed:29194485). kcat is 677 sec(-1) with NADH as substrate
CC         (PubMed:29194485). {ECO:0000269|PubMed:29194485};
CC   -!- SUBUNIT: Forms a homodimer (PubMed:29194485). Forms a disulfide-linked
CC       homodimer upon oxidation (PubMed:29194485). Interacts with 14-3-3-like
CC       proteins GRF1 GRF3 and GRF8 (PubMed:22104211). Interacts with TRX1,
CC       TRX2, TRX3, TRX4 and TRX5 (PubMed:29194485).
CC       {ECO:0000269|PubMed:22104211, ECO:0000269|PubMed:29194485}.
CC   -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000305}.
CC   -!- TISSUE SPECIFICITY: Expressed in rosette leaves.
CC       {ECO:0000269|PubMed:20876337}.
CC   -!- SIMILARITY: Belongs to the LDH/MDH superfamily. MDH type 2 family.
CC       {ECO:0000305}.
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DR   EMBL; AC000104; AAB70434.1; -; Genomic_DNA.
DR   EMBL; CP002684; AEE27694.1; -; Genomic_DNA.
DR   EMBL; AY050374; AAK91392.1; -; mRNA.
DR   EMBL; AY065134; AAL38310.1; -; mRNA.
DR   EMBL; AY081563; AAM10125.1; -; mRNA.
DR   EMBL; AY133655; AAM91485.1; -; mRNA.
DR   EMBL; AY088023; AAM65569.1; -; mRNA.
DR   PIR; B86176; B86176.
DR   RefSeq; NP_171936.1; NM_100321.3.
DR   PDB; 5NUE; X-ray; 1.35 A; A/B/C=1-332.
DR   PDB; 5NUF; X-ray; 1.80 A; A/B/C=1-332.
DR   PDBsum; 5NUE; -.
DR   PDBsum; 5NUF; -.
DR   AlphaFoldDB; P93819; -.
DR   SMR; P93819; -.
DR   BioGRID; 24762; 15.
DR   IntAct; P93819; 4.
DR   STRING; 3702.P93819; -.
DR   iPTMnet; P93819; -.
DR   MetOSite; P93819; -.
DR   PaxDb; 3702-AT1G04410-1; -.
DR   ProteomicsDB; 238771; -.
DR   EnsemblPlants; AT1G04410.1; AT1G04410.1; AT1G04410.
DR   GeneID; 839527; -.
DR   Gramene; AT1G04410.1; AT1G04410.1; AT1G04410.
DR   KEGG; ath:AT1G04410; -.
DR   Araport; AT1G04410; -.
DR   TAIR; AT1G04410; C-NAD-MDH1.
DR   eggNOG; KOG1496; Eukaryota.
DR   HOGENOM; CLU_040727_2_0_1; -.
DR   InParanoid; P93819; -.
DR   OMA; DHMRDWT; -.
DR   OrthoDB; 501358at2759; -.
DR   PhylomeDB; P93819; -.
DR   BRENDA; 1.1.1.37; 399.
DR   PRO; PR:P93819; -.
DR   Proteomes; UP000006548; Chromosome 1.
DR   ExpressionAtlas; P93819; baseline and differential.
DR   GO; GO:0048046; C:apoplast; HDA:TAIR.
DR   GO; GO:0009507; C:chloroplast; HDA:TAIR.
DR   GO; GO:0009570; C:chloroplast stroma; HDA:TAIR.
DR   GO; GO:0005829; C:cytosol; HDA:TAIR.
DR   GO; GO:0005576; C:extracellular region; HDA:TAIR.
DR   GO; GO:0005634; C:nucleus; HDA:TAIR.
DR   GO; GO:0000325; C:plant-type vacuole; HDA:TAIR.
DR   GO; GO:0005886; C:plasma membrane; HDA:TAIR.
DR   GO; GO:0009506; C:plasmodesma; HDA:TAIR.
DR   GO; GO:0030060; F:L-malate dehydrogenase activity; IEA:UniProtKB-EC.
DR   GO; GO:0003729; F:mRNA binding; IDA:TAIR.
DR   GO; GO:0006108; P:malate metabolic process; IEA:InterPro.
DR   GO; GO:0010043; P:response to zinc ion; IEP:TAIR.
DR   GO; GO:0006099; P:tricarboxylic acid cycle; IEA:UniProtKB-KW.
DR   CDD; cd01336; MDH_cytoplasmic_cytosolic; 1.
DR   Gene3D; 3.90.110.10; Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal; 1.
DR   Gene3D; 3.40.50.720; NAD(P)-binding Rossmann-like Domain; 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; IPR011274; Malate_DH_NAD-dep_euk.
DR   InterPro; IPR010945; Malate_DH_type2.
DR   InterPro; IPR036291; NAD(P)-bd_dom_sf.
DR   NCBIfam; TIGR01759; MalateDH-SF1; 1.
DR   NCBIfam; TIGR01758; MDH_euk_cyt; 1.
DR   PANTHER; PTHR23382; MALATE DEHYDROGENASE; 1.
DR   PANTHER; PTHR23382:SF27; MALATE DEHYDROGENASE 1, CYTOPLASMIC; 1.
DR   Pfam; PF02866; Ldh_1_C; 1.
DR   Pfam; PF00056; Ldh_1_N; 1.
DR   PIRSF; PIRSF000102; Lac_mal_DH; 1.
DR   SUPFAM; SSF56327; LDH C-terminal domain-like; 1.
DR   SUPFAM; SSF51735; NAD(P)-binding Rossmann-fold domains; 1.
DR   PROSITE; PS00068; MDH; 1.
DR   SWISS-2DPAGE; P93819; -.
DR   Genevisible; P93819; AT.
PE   1: Evidence at protein level;
KW   3D-structure; Cytoplasm; Disulfide bond; Isopeptide bond; NAD; Oxidation;
KW   Oxidoreductase; Reference proteome; Tricarboxylic acid cycle;
KW   Ubl conjugation.
FT   CHAIN           1..332
FT                   /note="Malate dehydrogenase 1, cytoplasmic"
FT                   /id="PRO_0000113412"
FT   ACT_SITE        188
FT                   /note="Proton acceptor"
FT                   /evidence="ECO:0000250|UniProtKB:P11708"
FT   BINDING         16..17
FT                   /ligand="NAD(+)"
FT                   /ligand_id="ChEBI:CHEBI:57540"
FT                   /evidence="ECO:0000269|PubMed:29194485,
FT                   ECO:0007744|PDB:5NUE, ECO:0007744|PDB:5NUF"
FT   BINDING         43
FT                   /ligand="NAD(+)"
FT                   /ligand_id="ChEBI:CHEBI:57540"
FT                   /evidence="ECO:0000269|PubMed:29194485,
FT                   ECO:0007744|PDB:5NUE, ECO:0007744|PDB:5NUF"
FT   BINDING         90
FT                   /ligand="NAD(+)"
FT                   /ligand_id="ChEBI:CHEBI:57540"
FT                   /evidence="ECO:0000269|PubMed:29194485,
FT                   ECO:0007744|PDB:5NUE, ECO:0007744|PDB:5NUF"
FT   BINDING         99
FT                   /ligand="oxaloacetate"
FT                   /ligand_id="ChEBI:CHEBI:16452"
FT                   /evidence="ECO:0000269|PubMed:29194485,
FT                   ECO:0007744|PDB:5NUE, ECO:0007744|PDB:5NUF"
FT   BINDING         113
FT                   /ligand="NAD(+)"
FT                   /ligand_id="ChEBI:CHEBI:57540"
FT                   /evidence="ECO:0000269|PubMed:29194485,
FT                   ECO:0007744|PDB:5NUE, ECO:0007744|PDB:5NUF"
FT   BINDING         132
FT                   /ligand="NAD(+)"
FT                   /ligand_id="ChEBI:CHEBI:57540"
FT                   /evidence="ECO:0000269|PubMed:29194485,
FT                   ECO:0007744|PDB:5NUE, ECO:0007744|PDB:5NUF"
FT   BINDING         132
FT                   /ligand="oxaloacetate"
FT                   /ligand_id="ChEBI:CHEBI:16452"
FT                   /evidence="ECO:0000269|PubMed:29194485,
FT                   ECO:0007744|PDB:5NUE, ECO:0007744|PDB:5NUF"
FT   BINDING         163
FT                   /ligand="oxaloacetate"
FT                   /ligand_id="ChEBI:CHEBI:16452"
FT                   /evidence="ECO:0000269|PubMed:29194485,
FT                   ECO:0007744|PDB:5NUE, ECO:0007744|PDB:5NUF"
FT   BINDING         188
FT                   /ligand="oxaloacetate"
FT                   /ligand_id="ChEBI:CHEBI:16452"
FT                   /evidence="ECO:0000269|PubMed:29194485,
FT                   ECO:0007744|PDB:5NUE, ECO:0007744|PDB:5NUF"
FT   BINDING         243
FT                   /ligand="oxaloacetate"
FT                   /ligand_id="ChEBI:CHEBI:16452"
FT                   /evidence="ECO:0000269|PubMed:29194485,
FT                   ECO:0007744|PDB:5NUE, ECO:0007744|PDB:5NUF"
FT   MOD_RES         56
FT                   /note="Methionine sulfoxide"
FT                   /evidence="ECO:0000269|PubMed:29194485"
FT   MOD_RES         97
FT                   /note="Methionine sulfoxide"
FT                   /evidence="ECO:0000269|PubMed:29194485"
FT   DISULFID        330
FT                   /note="Interchain; in linked form"
FT                   /evidence="ECO:0000269|PubMed:29194485"
FT   CROSSLNK        119
FT                   /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT                   G-Cter in ubiquitin)"
FT                   /evidence="ECO:0000269|PubMed:19292762"
FT   STRAND          6..11
FT                   /evidence="ECO:0007829|PDB:5NUE"
FT   TURN            12..14
FT                   /evidence="ECO:0007829|PDB:5NUE"
FT   HELIX           16..26
FT                   /evidence="ECO:0007829|PDB:5NUE"
FT   TURN            27..31
FT                   /evidence="ECO:0007829|PDB:5NUE"
FT   STRAND          37..42
FT                   /evidence="ECO:0007829|PDB:5NUE"
FT   HELIX           45..47
FT                   /evidence="ECO:0007829|PDB:5NUE"
FT   HELIX           48..60
FT                   /evidence="ECO:0007829|PDB:5NUE"
FT   STRAND          66..73
FT                   /evidence="ECO:0007829|PDB:5NUE"
FT   HELIX           75..79
FT                   /evidence="ECO:0007829|PDB:5NUE"
FT   STRAND          83..87
FT                   /evidence="ECO:0007829|PDB:5NUE"
FT   HELIX           99..120
FT                   /evidence="ECO:0007829|PDB:5NUE"
FT   STRAND          126..129
FT                   /evidence="ECO:0007829|PDB:5NUE"
FT   STRAND          131..133
FT                   /evidence="ECO:0007829|PDB:5NUE"
FT   HELIX           134..144
FT                   /evidence="ECO:0007829|PDB:5NUE"
FT   HELIX           150..152
FT                   /evidence="ECO:0007829|PDB:5NUE"
FT   STRAND          153..155
FT                   /evidence="ECO:0007829|PDB:5NUE"
FT   HELIX           158..172
FT                   /evidence="ECO:0007829|PDB:5NUE"
FT   HELIX           176..178
FT                   /evidence="ECO:0007829|PDB:5NUE"
FT   STRAND          183..186
FT                   /evidence="ECO:0007829|PDB:5NUE"
FT   STRAND          193..195
FT                   /evidence="ECO:0007829|PDB:5NUE"
FT   STRAND          200..203
FT                   /evidence="ECO:0007829|PDB:5NUE"
FT   STRAND          206..209
FT                   /evidence="ECO:0007829|PDB:5NUE"
FT   HELIX           210..214
FT                   /evidence="ECO:0007829|PDB:5NUE"
FT   HELIX           217..220
FT                   /evidence="ECO:0007829|PDB:5NUE"
FT   HELIX           223..239
FT                   /evidence="ECO:0007829|PDB:5NUE"
FT   HELIX           245..260
FT                   /evidence="ECO:0007829|PDB:5NUE"
FT   STRAND          268..273
FT                   /evidence="ECO:0007829|PDB:5NUE"
FT   HELIX           277..279
FT                   /evidence="ECO:0007829|PDB:5NUE"
FT   STRAND          284..293
FT                   /evidence="ECO:0007829|PDB:5NUE"
FT   STRAND          296..299
FT                   /evidence="ECO:0007829|PDB:5NUE"
FT   HELIX           307..330
FT                   /evidence="ECO:0007829|PDB:5NUE"
SQ   SEQUENCE   332 AA;  35571 MW;  C85D11E2BDFF556D CRC64;
     MAKEPVRVLV TGAAGQIGYA LVPMIARGIM LGADQPVILH MLDIPPAAEA LNGVKMELID
     AAFPLLKGVV ATTDAVEGCT GVNVAVMVGG FPRKEGMERK DVMSKNVSIY KSQAAALEKH
     AAPNCKVLVV ANPANTNALI LKEFAPSIPE KNISCLTRLD HNRALGQISE RLSVPVSDVK
     NVIIWGNHSS SQYPDVNHAK VQTSSGEKPV RELVKDDAWL DGEFISTVQQ RGAAIIKARK
     LSSALSAASS ACDHIRDWVL GTPEGTFVSM GVYSDGSYSV PSGLIYSFPV TCRNGDWSIV
     QGLPIDEVSR KKMDLTAEEL KEEKDLAYSC LS
//