ID   MDHG_ORYSJ              Reviewed;         356 AA.
AC   Q42972; B7E6W8; Q2QLQ8; Q2QLQ9;
DT   15-JUL-1998, integrated into UniProtKB/Swiss-Prot.
DT   25-JUL-2006, sequence version 3.
DT   27-MAR-2024, entry version 157.
DE   RecName: Full=Malate dehydrogenase, glyoxysomal;
DE            EC=1.1.1.37;
DE   Flags: Precursor;
GN   OrderedLocusNames=Os12g0632700, LOC_Os12g43630;
GN   ORFNames=OsJ_36976 {ECO:0000312|EMBL:EEE53658.1};
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].
RC   STRAIN=cv. Nipponbare;
RA   Kaminaka H., Morita S., Masumura T., Tanaka K.;
RT   "Molecular cloning and characterization of a cDNA encoding Glyoxysomal
RT   malate dehydrogenase from rice (Oryza sativa L.).";
RL   (er) Plant Gene Register PGR98-161(1998).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=cv. Nipponbare;
RX   PubMed=16188032; DOI=10.1186/1741-7007-3-20;
RG   The rice chromosomes 11 and 12 sequencing consortia;
RT   "The sequence of rice chromosomes 11 and 12, rich in disease resistance
RT   genes and recent gene duplications.";
RL   BMC Biol. 3:20-20(2005).
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   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=cv. Nipponbare;
RX   PubMed=15685292; DOI=10.1371/journal.pbio.0030038;
RA   Yu J., Wang J., Lin W., Li S., Li H., Zhou J., Ni P., Dong W., Hu S.,
RA   Zeng C., Zhang J., Zhang Y., Li R., Xu Z., Li S., Li X., Zheng H., Cong L.,
RA   Lin L., Yin J., Geng J., Li G., Shi J., Liu J., Lv H., Li J., Wang J.,
RA   Deng Y., Ran L., Shi X., Wang X., Wu Q., Li C., Ren X., Wang J., Wang X.,
RA   Li D., Liu D., Zhang X., Ji Z., Zhao W., Sun Y., Zhang Z., Bao J., Han Y.,
RA   Dong L., Ji J., Chen P., Wu S., Liu J., Xiao Y., Bu D., Tan J., Yang L.,
RA   Ye C., Zhang J., Xu J., Zhou Y., Yu Y., Zhang B., Zhuang S., Wei H.,
RA   Liu B., Lei M., Yu H., Li Y., Xu H., Wei S., He X., Fang L., Zhang Z.,
RA   Zhang Y., Huang X., Su Z., Tong W., Li J., Tong Z., Li S., Ye J., Wang L.,
RA   Fang L., Lei T., Chen C.-S., Chen H.-C., Xu Z., Li H., Huang H., Zhang F.,
RA   Xu H., Li N., Zhao C., Li S., Dong L., Huang Y., Li L., Xi Y., Qi Q.,
RA   Li W., Zhang B., Hu W., Zhang Y., Tian X., Jiao Y., Liang X., Jin J.,
RA   Gao L., Zheng W., Hao B., Liu S.-M., Wang W., Yuan L., Cao M.,
RA   McDermott J., Samudrala R., Wang J., Wong G.K.-S., Yang H.;
RT   "The genomes of Oryza sativa: a history of duplications.";
RL   PLoS Biol. 3:266-281(2005).
RN   [7]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC   STRAIN=cv. Nipponbare;
RX   PubMed=12869764; DOI=10.1126/science.1081288;
RG   The rice full-length cDNA consortium;
RT   "Collection, mapping, and annotation of over 28,000 cDNA clones from
RT   japonica rice.";
RL   Science 301:376-379(2003).
RN   [8]
RP   PROTEIN SEQUENCE [LARGE SCALE ANALYSIS] OF 37-43, AND IDENTIFICATION BY
RP   MASS SPECTROMETRY.
RC   STRAIN=cv. Nipponbare;
RX   PubMed=16758443; DOI=10.1002/pmic.200600043;
RA   Nozu Y., Tsugita A., Kamijo K.;
RT   "Proteomic analysis of rice leaf, stem and root tissues during growth
RT   course.";
RL   Proteomics 6:3665-3670(2006).
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.
CC   -!- SUBCELLULAR LOCATION: Glyoxysome.
CC   -!- SIMILARITY: Belongs to the LDH/MDH superfamily. MDH type 1 family.
CC       {ECO:0000305}.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=ABA99939.2; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR   EMBL; D85763; BAA12870.1; -; mRNA.
DR   EMBL; DP000011; ABA99938.2; -; Genomic_DNA.
DR   EMBL; DP000011; ABA99939.2; ALT_SEQ; Genomic_DNA.
DR   EMBL; AP008218; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR   EMBL; AP014968; BAT18226.1; -; Genomic_DNA.
DR   EMBL; CM000149; EEE53658.1; -; Genomic_DNA.
DR   EMBL; AK061793; BAG88115.1; -; mRNA.
DR   EMBL; AK065955; BAG89751.1; -; mRNA.
DR   PIR; T03272; T03272.
DR   RefSeq; XP_015620524.1; XM_015765038.1.
DR   AlphaFoldDB; Q42972; -.
DR   SMR; Q42972; -.
DR   STRING; 39947.Q42972; -.
DR   PaxDb; 39947-Q42972; -.
DR   EnsemblPlants; Os12t0632700-01; Os12t0632700-01; Os12g0632700.
DR   GeneID; 4352871; -.
DR   Gramene; Os12t0632700-01; Os12t0632700-01; Os12g0632700.
DR   KEGG; osa:4352871; -.
DR   eggNOG; KOG1494; Eukaryota.
DR   HOGENOM; CLU_047181_0_2_1; -.
DR   InParanoid; Q42972; -.
DR   OMA; IVNAHGV; -.
DR   OrthoDB; 5059897at2759; -.
DR   Proteomes; UP000000763; Chromosome 12.
DR   Proteomes; UP000007752; Chromosome 12.
DR   Proteomes; UP000059680; Chromosome 12.
DR   GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR   GO; GO:0009514; C:glyoxysome; IEA:UniProtKB-SubCell.
DR   GO; GO:0030060; F:L-malate dehydrogenase activity; IBA:GO_Central.
DR   GO; GO:0006097; P:glyoxylate cycle; IEA:UniProtKB-KW.
DR   GO; GO:0006108; P:malate metabolic process; IEA:InterPro.
DR   GO; GO:0006099; P:tricarboxylic acid cycle; IEA:UniProtKB-KW.
DR   CDD; cd01337; MDH_glyoxysomal_mitochondrial; 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; IPR010097; Malate_DH_type1.
DR   InterPro; IPR036291; NAD(P)-bd_dom_sf.
DR   NCBIfam; TIGR01772; MDH_euk_gproteo; 1.
DR   PANTHER; PTHR11540; MALATE AND LACTATE DEHYDROGENASE; 1.
DR   PANTHER; PTHR11540:SF52; MALATE DEHYDROGENASE 2, PEROXISOMAL; 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   Genevisible; Q42972; OS.
PE   1: Evidence at protein level;
KW   Direct protein sequencing; Glyoxylate bypass; Glyoxysome; NAD;
KW   Oxidoreductase; Peroxisome; Reference proteome; Transit peptide;
KW   Tricarboxylic acid cycle.
FT   TRANSIT         1..36
FT                   /note="Glyoxysome"
FT                   /evidence="ECO:0000269|PubMed:16758443"
FT   CHAIN           37..356
FT                   /note="Malate dehydrogenase, glyoxysomal"
FT                   /id="PRO_0000018640"
FT   ACT_SITE        220
FT                   /note="Proton acceptor"
FT                   /evidence="ECO:0000250"
FT   BINDING         51..57
FT                   /ligand="NAD(+)"
FT                   /ligand_id="ChEBI:CHEBI:57540"
FT                   /evidence="ECO:0000250"
FT   BINDING         77
FT                   /ligand="NAD(+)"
FT                   /ligand_id="ChEBI:CHEBI:57540"
FT                   /evidence="ECO:0000250"
FT   BINDING         124
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU10004"
FT   BINDING         130
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU10004"
FT   BINDING         137
FT                   /ligand="NAD(+)"
FT                   /ligand_id="ChEBI:CHEBI:57540"
FT                   /evidence="ECO:0000250"
FT   BINDING         160..162
FT                   /ligand="NAD(+)"
FT                   /ligand_id="ChEBI:CHEBI:57540"
FT                   /evidence="ECO:0000250"
FT   BINDING         162
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU10004"
FT   BINDING         196
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU10004"
FT   BINDING         271
FT                   /ligand="NAD(+)"
FT                   /ligand_id="ChEBI:CHEBI:57540"
FT                   /evidence="ECO:0000250"
SQ   SEQUENCE   356 AA;  37385 MW;  D57BD93E93F381FB CRC64;
     MEDAAAAARR MERLASHLRP PASQMEESPL LRGSNCRAKG AAPGFKVAIL GASGGIGQPL
     ALLMKMNPLV SVLHLYDVVN TPGVTADISH MNTGAVVRGF LGQPQLENAL TGMDLVIIPA
     GVPRKPGMTR DDLFNINAGI VRTLCEGIAK CCPNAIVNVI SNPVNSTVPI AAEVFKKAGT
     YDPKRLLGVT TLDVVRANTF VAEVLGLDPR DVNVPVIGGH AGVTILPLLS QVNPPCSFTS
     EEISYLTTRI QNGGTEVVEA KAGAGSATLS MAYAASKFAD ACLRGLRGDA GIVECSFVAS
     QVTELPFFAS KVRLGRCGIE EILSLGPLNE FERAGLEKAK KELAESIQKG VAFINK
//