MDHC_ORYSJ
ID MDHC_ORYSJ Reviewed; 332 AA.
AC Q7XDC8; Q0IWZ1; Q109J3; Q9FWH5;
DT 20-DEC-2005, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 3.
DT 03-AUG-2022, entry version 124.
DE RecName: Full=Malate dehydrogenase, cytoplasmic;
DE EC=1.1.1.37;
DE AltName: Full=PP37;
GN OrderedLocusNames=Os10g0478200, LOC_Os10g33800; ORFNames=OSJNBa0055P24.3;
OS Oryza sativa subsp. japonica (Rice).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade;
OC Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa.
OX NCBI_TaxID=39947;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA], AND TISSUE SPECIFICITY.
RX PubMed=15620222; DOI=10.1080/10425170410001710565;
RA Lin C.F., Jiang R.H., Jiang L.Z., Qian X.Y., Attia K., Yang J.S.;
RT "Cloning, characterization and prokaryotic expression of cytosolic malate
RT dehydrogenase from Oryza sativa.";
RL DNA Seq. 15:314-318(2004).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=12791992; DOI=10.1126/science.1083523;
RA Yu Y., Rambo T., Currie J., Saski C., Kim H.-R., Collura K., Thompson S.,
RA Simmons J., Yang T.-J., Nah G., Patel A.J., Thurmond S., Henry D.,
RA Oates R., Palmer M., Pries G., Gibson J., Anderson H., Paradkar M.,
RA Crane L., Dale J., Carver M.B., Wood T., Frisch D., Engler F.,
RA Soderlund C., Palmer L.E., Teytelman L., Nascimento L., De la Bastide M.,
RA Spiegel L., Ware D., O'Shaughnessy A., Dike S., Dedhia N., Preston R.,
RA Huang E., Ferraro K., Kuit K., Miller B., Zutavern T., Katzenberger F.,
RA Muller S., Balija V., Martienssen R.A., Stein L., Minx P., Johnson D.,
RA Cordum H., Mardis E., Cheng Z., Jiang J., Wilson R., McCombie W.R.,
RA Wing R.A., Yuan Q., Ouyang S., Liu J., Jones K.M., Gansberger K.,
RA Moffat K., Hill J., Tsitrin T., Overton L., Bera J., Kim M., Jin S.,
RA Tallon L., Ciecko A., Pai G., Van Aken S., Utterback T., Reidmuller S.,
RA Bormann J., Feldblyum T., Hsiao J., Zismann V., Blunt S., de Vazeille A.R.,
RA Shaffer T., Koo H., Suh B., Yang Q., Haas B., Peterson J., Pertea M.,
RA Volfovsky N., Wortman J., White O., Salzberg S.L., Fraser C.M., Buell C.R.,
RA Messing J., Song R., Fuks G., Llaca V., Kovchak S., Young S., Bowers J.E.,
RA Paterson A.H., Johns M.A., Mao L., Pan H., Dean R.A.;
RT "In-depth view of structure, activity, and evolution of rice chromosome
RT 10.";
RL Science 300:1566-1569(2003).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16100779; DOI=10.1038/nature03895;
RG International rice genome sequencing project (IRGSP);
RT "The map-based sequence of the rice genome.";
RL Nature 436:793-800(2005).
RN [4]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=18089549; DOI=10.1093/nar/gkm978;
RG The rice annotation project (RAP);
RT "The rice annotation project database (RAP-DB): 2008 update.";
RL Nucleic Acids Res. 36:D1028-D1033(2008).
RN [5]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=24280374; DOI=10.1186/1939-8433-6-4;
RA Kawahara Y., de la Bastide M., Hamilton J.P., Kanamori H., McCombie W.R.,
RA Ouyang S., Schwartz D.C., Tanaka T., Wu J., Zhou S., Childs K.L.,
RA Davidson R.M., Lin H., Quesada-Ocampo L., Vaillancourt B., Sakai H.,
RA Lee S.S., Kim J., Numa H., Itoh T., Buell C.R., Matsumoto T.;
RT "Improvement of the Oryza sativa Nipponbare reference genome using next
RT generation sequence and optical map data.";
RL Rice 6:4-4(2013).
RN [6]
RP PROTEIN SEQUENCE OF 2-11; 41-50; 144-153 AND 151-160, AND TISSUE
RP SPECIFICITY.
RC STRAIN=cv. Nipponbare; TISSUE=Panicle, Sheath, and Stem;
RX PubMed=14681440; DOI=10.1093/nar/gkh020;
RA Komatsu S., Kojima K., Suzuki K., Ozaki K., Higo K.;
RT "Rice proteome database based on two-dimensional polyacrylamide gel
RT electrophoresis: its status in 2003.";
RL Nucleic Acids Res. 32:D388-D392(2004).
RN [7]
RP IDENTIFICATION BY MASS SPECTROMETRY, INDUCTION, AND PHOSPHORYLATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=16028114; DOI=10.1007/s11103-005-4013-1;
RA Khan M.M.K., Jan A., Karibe H., Komatsu S.;
RT "Identification of phosphoproteins regulated by gibberellin in rice leaf
RT sheath.";
RL Plant Mol. Biol. 58:27-40(2005).
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 -!- SUBUNIT: Homodimer. {ECO:0000250}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250}.
CC -!- TISSUE SPECIFICITY: Highly expressed in young panicles and immature
CC seeds. Weakly expressed in roots and leaves. Expressed in stem and
CC sheath (at protein level). {ECO:0000269|PubMed:14681440,
CC ECO:0000269|PubMed:15620222}.
CC -!- PTM: Phosphorylated after gibberellin treatment.
CC {ECO:0000269|PubMed:16028114}.
CC -!- SIMILARITY: Belongs to the LDH/MDH superfamily. MDH type 2 family.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=ABG66141.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AF353203; AAK26431.1; -; mRNA.
DR EMBL; AC037425; AAG13573.1; -; Genomic_DNA.
DR EMBL; DP000086; AAP54283.1; -; Genomic_DNA.
DR EMBL; DP000086; ABG66141.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AP008216; BAF26774.1; -; Genomic_DNA.
DR EMBL; AP014966; BAT11312.1; -; Genomic_DNA.
DR RefSeq; XP_015614294.1; XM_015758808.1.
DR AlphaFoldDB; Q7XDC8; -.
DR SMR; Q7XDC8; -.
DR STRING; 4530.OS10T0478200-01; -.
DR PaxDb; Q7XDC8; -.
DR PRIDE; Q7XDC8; -.
DR EnsemblPlants; Os10t0478200-01; Os10t0478200-01; Os10g0478200.
DR GeneID; 4348905; -.
DR Gramene; Os10t0478200-01; Os10t0478200-01; Os10g0478200.
DR KEGG; osa:4348905; -.
DR eggNOG; KOG1496; Eukaryota.
DR HOGENOM; CLU_040727_2_0_1; -.
DR InParanoid; Q7XDC8; -.
DR OMA; TKGMERG; -.
DR OrthoDB; 1118998at2759; -.
DR Proteomes; UP000000763; Chromosome 10.
DR Proteomes; UP000059680; Chromosome 10.
DR ExpressionAtlas; Q7XDC8; baseline and differential.
DR Genevisible; Q7XDC8; OS.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0030060; F:L-malate dehydrogenase activity; IBA:GO_Central.
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: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 Cytoplasm; Direct protein sequencing; NAD; Oxidoreductase; Phosphoprotein;
KW Reference proteome; Tricarboxylic acid cycle.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:14681440"
FT CHAIN 2..332
FT /note="Malate dehydrogenase, cytoplasmic"
FT /id="PRO_0000113418"
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:0000250|UniProtKB:P93819"
FT BINDING 43
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250|UniProtKB:P93819"
FT BINDING 90
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250|UniProtKB:P93819"
FT BINDING 99
FT /ligand="oxaloacetate"
FT /ligand_id="ChEBI:CHEBI:16452"
FT /evidence="ECO:0000250|UniProtKB:P93819"
FT BINDING 113
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250|UniProtKB:P93819"
FT BINDING 132
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250|UniProtKB:P93819"
FT BINDING 132
FT /ligand="oxaloacetate"
FT /ligand_id="ChEBI:CHEBI:16452"
FT /evidence="ECO:0000250|UniProtKB:P93819"
FT BINDING 163
FT /ligand="oxaloacetate"
FT /ligand_id="ChEBI:CHEBI:16452"
FT /evidence="ECO:0000250|UniProtKB:P93819"
FT BINDING 188
FT /ligand="oxaloacetate"
FT /ligand_id="ChEBI:CHEBI:16452"
FT /evidence="ECO:0000250|UniProtKB:P93819"
FT BINDING 243
FT /ligand="oxaloacetate"
FT /ligand_id="ChEBI:CHEBI:16452"
FT /evidence="ECO:0000250|UniProtKB:P93819"
SQ SEQUENCE 332 AA; 35569 MW; EB1E3187DCC4DF42 CRC64;
MAKEPMRVLV TGAAGQIGYA LVPMIARGVM LGADQPVILH MLDIPPATES LNGLKMELVD
AAFPLLKGIV ATTDVVEACT GVNVAVMVGG FPRKEGMERK DVMSKNVSIY KSQASALEAH
AAPNCKVLVV ANPANTNALI LKEFAPSIPE KNITCLTRLD HNRALGQISE KLNVQVTDVK
NAIIWGNHSS TQYPDVNHAT VKTPSGEKPV RELVADDEWL NTEFISTVQQ RGAAIIKARK
QSSALSAASS ACDHIRDWVL GTPEGTFVSM GVYSDGSYGV PAGLIYSFPV TCSGGEWTIV
QGLPIDEFSR KKMDATAQEL SEEKTLAYSC LN
