MDHC1_ARATH
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 03-AUG-2022, entry version 179.
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.AT1G04410.1; -.
DR iPTMnet; P93819; -.
DR MetOSite; P93819; -.
DR SWISS-2DPAGE; P93819; -.
DR PaxDb; P93819; -.
DR PRIDE; P93819; -.
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; locus:2018244; AT1G04410.
DR eggNOG; KOG1496; Eukaryota.
DR HOGENOM; CLU_040727_2_0_1; -.
DR InParanoid; P93819; -.
DR OMA; GMIGSNM; -.
DR OrthoDB; 1118998at2759; -.
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 Genevisible; P93819; AT.
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; IBA:GO_Central.
DR GO; GO:0003729; F:mRNA binding; IDA:TAIR.
DR GO; GO:0006108; P:malate metabolic process; IBA:GO_Central.
DR GO; GO:0006734; P:NADH metabolic process; IBA:GO_Central.
DR GO; GO:0006107; P:oxaloacetate metabolic process; IBA:GO_Central.
DR GO; GO:0010043; P:response to zinc ion; IEP:TAIR.
DR GO; GO:0006099; P:tricarboxylic acid cycle; IBA:GO_Central.
DR CDD; cd01336; MDH_cytoplasmic_cytosolic; 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; IPR011274; Malate_DH_NAD-dep_euk.
DR InterPro; IPR010945; Malate_DH_type2.
DR InterPro; IPR036291; NAD(P)-bd_dom_sf.
DR PANTHER; PTHR23382; PTHR23382; 1.
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; TIGR01759; MalateDH-SF1; 1.
DR TIGRFAMs; TIGR01758; MDH_euk_cyt; 1.
DR PROSITE; PS00068; MDH; 1.
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
