ID   MDHX1_ARATH             Reviewed;         354 AA.
AC   O82399;
DT   01-DEC-2000, integrated into UniProtKB/Swiss-Prot.
DT   01-NOV-1998, sequence version 1.
DT   27-MAR-2024, entry version 170.
DE   RecName: Full=Malate dehydrogenase 1, peroxisomal {ECO:0000305};
DE            EC=1.1.1.37;
DE   AltName: Full=Peroxisomal NAD-dependent malate dehydrogenase 1 {ECO:0000305};
DE            Short=pxNAD-MDH1 {ECO:0000303|PubMed:20876337};
DE   AltName: Full=Peroxisomal malate dehydrogenase 1 {ECO:0000303|PubMed:20876337};
DE            Short=Peroxisomal MDH1 {ECO:0000305};
GN   Name=PMDH1 {ECO:0000303|PubMed:17376163}; OrderedLocusNames=At2g22780;
GN   ORFNames=T30L20.4;
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=10617197; DOI=10.1038/45471;
RA   Lin X., Kaul S., Rounsley S.D., Shea T.P., Benito M.-I., Town C.D.,
RA   Fujii C.Y., Mason T.M., Bowman C.L., Barnstead M.E., Feldblyum T.V.,
RA   Buell C.R., Ketchum K.A., Lee J.J., Ronning C.M., Koo H.L., Moffat K.S.,
RA   Cronin L.A., Shen M., Pai G., Van Aken S., Umayam L., Tallon L.J.,
RA   Gill J.E., Adams M.D., Carrera A.J., Creasy T.H., Goodman H.M.,
RA   Somerville C.R., Copenhaver G.P., Preuss D., Nierman W.C., White O.,
RA   Eisen J.A., Salzberg S.L., Fraser C.M., Venter J.C.;
RT   "Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana.";
RL   Nature 402:761-768(1999).
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   IDENTIFICATION BY MASS SPECTROMETRY.
RX   PubMed=17951448; DOI=10.1105/tpc.107.050989;
RA   Reumann S., Babujee L., Ma C., Wienkoop S., Siemsen T., Antonicelli G.E.,
RA   Rasche N., Lueder F., Weckwerth W., Jahn O.;
RT   "Proteome analysis of Arabidopsis leaf peroxisomes reveals novel targeting
RT   peptides, metabolic pathways, and defense mechanisms.";
RL   Plant Cell 19:3170-3193(2007).
RN   [5]
RP   FUNCTION, SUBCELLULAR LOCATION, AND DISRUPTION PHENOTYPE.
RX   PubMed=17376163; DOI=10.1111/j.1365-313x.2007.03055.x;
RA   Pracharoenwattana I., Cornah J.E., Smith S.M.;
RT   "Arabidopsis peroxisomal malate dehydrogenase functions in beta-oxidation
RT   but not in the glyoxylate cycle.";
RL   Plant J. 50:381-390(2007).
RN   [6]
RP   FUNCTION.
RX   PubMed=18685043; DOI=10.1104/pp.108.122622;
RA   Cousins A.B., Pracharoenwattana I., Zhou W., Smith S.M., Badger M.R.;
RT   "Peroxisomal malate dehydrogenase is not essential for photorespiration in
RT   Arabidopsis but its absence causes an increase in the stoichiometry of
RT   photorespiratory CO2 release.";
RL   Plant Physiol. 148:786-795(2008).
RN   [7]
RP   FUNCTION.
RX   PubMed=19812894; DOI=10.1007/s11103-009-9554-2;
RA   Pracharoenwattana I., Zhou W., Smith S.M.;
RT   "Fatty acid beta-oxidation in germinating Arabidopsis seeds is supported by
RT   peroxisomal hydroxypyruvate reductase when malate dehydrogenase is
RT   absent.";
RL   Plant Mol. Biol. 72:101-109(2010).
RN   [8]
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).
CC   -!- FUNCTION: Catalyzes a reversible NAD-dependent dehydrogenase reaction
CC       involved in central metabolism and redox homeostasis between organelle
CC       compartments (Probable). Peroxisomal NAD-dependent malate dehydrogenase
CC       involved in fatty acid beta-oxidation. Reoxidizes NADH from the beta-
CC       oxidation and provides NAD for the conversion of fatty acyl-CoA to
CC       acetyl-CoA. Does not participate directly in the glyoxylate cycle
CC       (PubMed:17376163, PubMed:19812894). Required for maintenance of
CC       photosynthetic rates under photorespiratory conditions, and carbon flow
CC       during photorespiration. Supplies NADH reductant to the peroxisomal
CC       hydroxypyruvate reductase (HPR), which reduces hydroxypyruvate into
CC       glycerate in the photorespiratory cycle (PubMed:18685043).
CC       {ECO:0000269|PubMed:17376163, ECO:0000269|PubMed:18685043,
CC       ECO:0000269|PubMed:19812894, 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   -!- SUBUNIT: Homodimer. {ECO:0000250}.
CC   -!- SUBCELLULAR LOCATION: Peroxisome {ECO:0000269|PubMed:17376163}.
CC   -!- TISSUE SPECIFICITY: Expressed in rosette leaves at low levels.
CC       {ECO:0000269|PubMed:20876337}.
CC   -!- DISRUPTION PHENOTYPE: No visible phenotype under normal growth
CC       conditions, but the double mutant plants pmdh1 and pmdh2 show seedling
CC       growth arrest 5 days after seed imbibition.
CC       {ECO:0000269|PubMed:17376163}.
CC   -!- SIMILARITY: Belongs to the LDH/MDH superfamily. MDH type 1 family.
CC       {ECO:0000305}.
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DR   EMBL; AC005617; AAC63589.1; -; Genomic_DNA.
DR   EMBL; CP002685; AEC07353.1; -; Genomic_DNA.
DR   EMBL; AF428346; AAL16276.1; -; mRNA.
DR   EMBL; BT003009; AAO23574.1; -; mRNA.
DR   PIR; G84616; G84616.
DR   RefSeq; NP_179863.1; NM_127843.5.
DR   AlphaFoldDB; O82399; -.
DR   SMR; O82399; -.
DR   BioGRID; 2161; 2.
DR   IntAct; O82399; 1.
DR   STRING; 3702.O82399; -.
DR   PaxDb; 3702-AT2G22780-1; -.
DR   ProteomicsDB; 238334; -.
DR   EnsemblPlants; AT2G22780.1; AT2G22780.1; AT2G22780.
DR   GeneID; 816808; -.
DR   Gramene; AT2G22780.1; AT2G22780.1; AT2G22780.
DR   KEGG; ath:AT2G22780; -.
DR   Araport; AT2G22780; -.
DR   TAIR; AT2G22780; PMDH1.
DR   eggNOG; KOG1494; Eukaryota.
DR   HOGENOM; CLU_047181_0_2_1; -.
DR   InParanoid; O82399; -.
DR   OMA; IVNAHGV; -.
DR   OrthoDB; 5059897at2759; -.
DR   PhylomeDB; O82399; -.
DR   BioCyc; ARA:AT2G22780-MONOMER; -.
DR   BioCyc; MetaCyc:AT2G22780-MONOMER; -.
DR   PRO; PR:O82399; -.
DR   Proteomes; UP000006548; Chromosome 2.
DR   ExpressionAtlas; O82399; baseline and differential.
DR   GO; GO:0009507; C:chloroplast; HDA:TAIR.
DR   GO; GO:0005777; C:peroxisome; IDA:TAIR.
DR   GO; GO:0030060; F:L-malate dehydrogenase activity; IEA:UniProtKB-EC.
DR   GO; GO:0006097; P:glyoxylate cycle; IEA:UniProtKB-KW.
DR   GO; GO:0006108; P:malate metabolic process; IEA:InterPro.
DR   GO; GO:0031998; P:regulation of fatty acid beta-oxidation; IMP:TAIR.
DR   GO; GO:0080093; P:regulation of photorespiration; IMP:TAIR.
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:SF71; MALATE DEHYDROGENASE 1, 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; O82399; AT.
PE   1: Evidence at protein level;
KW   Glyoxylate bypass; NAD; Oxidoreductase; Peroxisome; Reference proteome;
KW   Tricarboxylic acid cycle.
FT   CHAIN           1..354
FT                   /note="Malate dehydrogenase 1, peroxisomal"
FT                   /id="PRO_0000018635"
FT   REGION          6..14
FT                   /note="Peroxisomal targeting signal PTS2"
FT                   /evidence="ECO:0000305|PubMed:17376163"
FT   ACT_SITE        218
FT                   /note="Proton acceptor"
FT                   /evidence="ECO:0000250|UniProtKB:P11708"
FT   BINDING         49..55
FT                   /ligand="NAD(+)"
FT                   /ligand_id="ChEBI:CHEBI:57540"
FT                   /evidence="ECO:0000250|UniProtKB:P40926"
FT   BINDING         75
FT                   /ligand="NAD(+)"
FT                   /ligand_id="ChEBI:CHEBI:57540"
FT                   /evidence="ECO:0000250|UniProtKB:P40926"
FT   BINDING         122
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000250|UniProtKB:P11708"
FT   BINDING         128
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000250|UniProtKB:P11708"
FT   BINDING         135
FT                   /ligand="NAD(+)"
FT                   /ligand_id="ChEBI:CHEBI:57540"
FT                   /evidence="ECO:0000250|UniProtKB:P40926"
FT   BINDING         158..160
FT                   /ligand="NAD(+)"
FT                   /ligand_id="ChEBI:CHEBI:57540"
FT                   /evidence="ECO:0000250|UniProtKB:P40926"
FT   BINDING         160
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000250|UniProtKB:P11708"
FT   BINDING         194
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000250|UniProtKB:P11708"
FT   BINDING         269
FT                   /ligand="NAD(+)"
FT                   /ligand_id="ChEBI:CHEBI:57540"
FT                   /evidence="ECO:0000250|UniProtKB:P40926"
SQ   SEQUENCE   354 AA;  37466 MW;  715CDC22B4448629 CRC64;
     MDPNQRIARI SAHLNPPNLH NQIADGSGLN RVACRAKGGS PGFKVAILGA AGGIGQPLAM
     LMKMNPLVSV LHLYDVANAP GVTADISHMD TSAVVRGFLG QPQLEEALTG MDLVIIPAGV
     PRKPGMTRDD LFNINAGIVR TLSEAIAKCC PKAIVNIISN PVNSTVPIAA EVFKKAGTFD
     PKKLMGVTML DVVRANTFVA EVMSLDPREV EVPVVGGHAG VTILPLLSQV KPPCSFTQKE
     IEYLTDRIQN GGTEVVEAKA GAGSATLSMA YAAVEFADAC LRGLRGDANI VECAYVASHV
     TELPFFASKV RLGRCGIDEV YGLGPLNEYE RMGLEKAKKE LSVSIHKGVT FAKK
//