MDHP_YEAST
ID MDHP_YEAST Reviewed; 343 AA.
AC P32419; D6VRS1; Q12689;
DT 01-OCT-1993, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 3.
DT 03-AUG-2022, entry version 188.
DE RecName: Full=Malate dehydrogenase, peroxisomal;
DE EC=1.1.1.37;
GN Name=MDH3; OrderedLocusNames=YDL078C; ORFNames=D2468;
OS Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX NCBI_TaxID=559292;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND PROTEIN SEQUENCE OF 2-16; 23-36 AND
RP 153-167.
RX PubMed=1447211; DOI=10.1016/s0021-9258(18)35822-8;
RA Steffan J.S., McAlister-Henn L.;
RT "Isolation and characterization of the yeast gene encoding the MDH3 isozyme
RT of malate dehydrogenase.";
RL J. Biol. Chem. 267:24708-24715(1992).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169867;
RA Jacq C., Alt-Moerbe J., Andre B., Arnold W., Bahr A., Ballesta J.P.G.,
RA Bargues M., Baron L., Becker A., Biteau N., Bloecker H., Blugeon C.,
RA Boskovic J., Brandt P., Brueckner M., Buitrago M.J., Coster F.,
RA Delaveau T., del Rey F., Dujon B., Eide L.G., Garcia-Cantalejo J.M.,
RA Goffeau A., Gomez-Peris A., Granotier C., Hanemann V., Hankeln T.,
RA Hoheisel J.D., Jaeger W., Jimenez A., Jonniaux J.-L., Kraemer C.,
RA Kuester H., Laamanen P., Legros Y., Louis E.J., Moeller-Rieker S.,
RA Monnet A., Moro M., Mueller-Auer S., Nussbaumer B., Paricio N., Paulin L.,
RA Perea J., Perez-Alonso M., Perez-Ortin J.E., Pohl T.M., Prydz H.,
RA Purnelle B., Rasmussen S.W., Remacha M.A., Revuelta J.L., Rieger M.,
RA Salom D., Saluz H.P., Saiz J.E., Saren A.-M., Schaefer M., Scharfe M.,
RA Schmidt E.R., Schneider C., Scholler P., Schwarz S., Soler-Mira A.,
RA Urrestarazu L.A., Verhasselt P., Vissers S., Voet M., Volckaert G.,
RA Wagner G., Wambutt R., Wedler E., Wedler H., Woelfl S., Harris D.E.,
RA Bowman S., Brown D., Churcher C.M., Connor R., Dedman K., Gentles S.,
RA Hamlin N., Hunt S., Jones L., McDonald S., Murphy L.D., Niblett D.,
RA Odell C., Oliver K., Rajandream M.A., Richards C., Shore L., Walsh S.V.,
RA Barrell B.G., Dietrich F.S., Mulligan J.T., Allen E., Araujo R., Aviles E.,
RA Berno A., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M.,
RA Hunicke-Smith S., Hyman R.W., Komp C., Lashkari D., Lew H., Lin D.,
RA Mosedale D., Nakahara K., Namath A., Oefner P., Oh C., Petel F.X.,
RA Roberts D., Schramm S., Schroeder M., Shogren T., Shroff N., Winant A.,
RA Yelton M.A., Botstein D., Davis R.W., Johnston M., Andrews S., Brinkman R.,
RA Cooper J., Ding H., Du Z., Favello A., Fulton L., Gattung S., Greco T.,
RA Hallsworth K., Hawkins J., Hillier L.W., Jier M., Johnson D., Johnston L.,
RA Kirsten J., Kucaba T., Langston Y., Latreille P., Le T., Mardis E.,
RA Menezes S., Miller N., Nhan M., Pauley A., Peluso D., Rifkin L., Riles L.,
RA Taich A., Trevaskis E., Vignati D., Wilcox L., Wohldman P., Vaudin M.,
RA Wilson R., Waterston R., Albermann K., Hani J., Heumann K., Kleine K.,
RA Mewes H.-W., Zollner A., Zaccaria P.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome IV.";
RL Nature 387:75-78(1997).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=24374639; DOI=10.1534/g3.113.008995;
RA Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
RA Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
RA Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.;
RT "The reference genome sequence of Saccharomyces cerevisiae: Then and now.";
RL G3 (Bethesda) 4:389-398(2014).
RN [4]
RP LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
RX PubMed=14562106; DOI=10.1038/nature02046;
RA Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N.,
RA O'Shea E.K., Weissman J.S.;
RT "Global analysis of protein expression in yeast.";
RL Nature 425:737-741(2003).
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: Peroxisome.
CC -!- MISCELLANEOUS: Yeast contains at least 3 malate dehydrogenase
CC isoenzymes: a mitochondrial (MDH1), a cytoplasmic (MDH2) and a
CC peroxisomal (MDH3).
CC -!- MISCELLANEOUS: Present with 3300 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the LDH/MDH superfamily. MDH type 1 family.
CC {ECO:0000305}.
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DR EMBL; M98763; AAA34767.1; -; Genomic_DNA.
DR EMBL; Z74126; CAA98644.1; -; Genomic_DNA.
DR EMBL; BK006938; DAA11781.1; -; Genomic_DNA.
DR PIR; S67614; DEBYMP.
DR RefSeq; NP_010205.1; NM_001180137.1.
DR PDB; 5ZI2; X-ray; 2.00 A; A/B=1-343.
DR PDB; 5ZI3; X-ray; 2.10 A; A/B=1-343.
DR PDB; 5ZI4; X-ray; 2.10 A; A/B=1-343.
DR PDBsum; 5ZI2; -.
DR PDBsum; 5ZI3; -.
DR PDBsum; 5ZI4; -.
DR AlphaFoldDB; P32419; -.
DR SMR; P32419; -.
DR BioGRID; 31983; 167.
DR DIP; DIP-6473N; -.
DR IntAct; P32419; 7.
DR MINT; P32419; -.
DR STRING; 4932.YDL078C; -.
DR iPTMnet; P32419; -.
DR UCD-2DPAGE; P32419; -.
DR MaxQB; P32419; -.
DR PaxDb; P32419; -.
DR PRIDE; P32419; -.
DR EnsemblFungi; YDL078C_mRNA; YDL078C; YDL078C.
DR GeneID; 851481; -.
DR KEGG; sce:YDL078C; -.
DR SGD; S000002236; MDH3.
DR VEuPathDB; FungiDB:YDL078C; -.
DR eggNOG; KOG1494; Eukaryota.
DR GeneTree; ENSGT00940000176501; -.
DR HOGENOM; CLU_047181_1_1_1; -.
DR InParanoid; P32419; -.
DR OMA; VECTFVQ; -.
DR BioCyc; YEAST:YDL078C-MON; -.
DR PRO; PR:P32419; -.
DR Proteomes; UP000002311; Chromosome IV.
DR RNAct; P32419; protein.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0005739; C:mitochondrion; IBA:GO_Central.
DR GO; GO:0005782; C:peroxisomal matrix; IDA:SGD.
DR GO; GO:0005777; C:peroxisome; IDA:SGD.
DR GO; GO:0030060; F:L-malate dehydrogenase activity; IDA:SGD.
DR GO; GO:0003729; F:mRNA binding; IDA:SGD.
DR GO; GO:0006635; P:fatty acid beta-oxidation; IMP:SGD.
DR GO; GO:0006097; P:glyoxylate cycle; IEA:UniProtKB-KW.
DR GO; GO:0006108; P:malate metabolic process; IEA:InterPro.
DR GO; GO:0006735; P:NADH regeneration; IMP:SGD.
DR GO; GO:0006099; P:tricarboxylic acid cycle; IBA:GO_Central.
DR CDD; cd01337; MDH_glyoxysomal_mitochondrial; 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; IPR010097; Malate_DH_type1.
DR InterPro; IPR036291; NAD(P)-bd_dom_sf.
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; TIGR01772; MDH_euk_gproteo; 1.
DR PROSITE; PS00068; MDH; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Direct protein sequencing; Glyoxylate bypass; NAD;
KW Oxidoreductase; Peroxisome; Reference proteome; Tricarboxylic acid cycle.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:1447211"
FT CHAIN 2..343
FT /note="Malate dehydrogenase, peroxisomal"
FT /id="PRO_0000113342"
FT ACT_SITE 187
FT /note="Proton acceptor"
FT /evidence="ECO:0000250|UniProtKB:P00346"
FT BINDING 8..14
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250|UniProtKB:P40926"
FT BINDING 34
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250|UniProtKB:P40926"
FT BINDING 80
FT /ligand="substrate"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10004"
FT BINDING 86
FT /ligand="substrate"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10004"
FT BINDING 93
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250|UniProtKB:P40926"
FT BINDING 116..118
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250|UniProtKB:P40926"
FT BINDING 118
FT /ligand="substrate"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10004"
FT BINDING 152
FT /ligand="substrate"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10004"
FT BINDING 237
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250|UniProtKB:P40926"
FT CONFLICT 240
FT /note="A -> R (in Ref. 1; AAA34767)"
FT /evidence="ECO:0000305"
FT STRAND 2..8
FT /evidence="ECO:0007829|PDB:5ZI2"
FT HELIX 14..23
FT /evidence="ECO:0007829|PDB:5ZI2"
FT STRAND 27..33
FT /evidence="ECO:0007829|PDB:5ZI2"
FT STRAND 35..37
FT /evidence="ECO:0007829|PDB:5ZI2"
FT HELIX 38..46
FT /evidence="ECO:0007829|PDB:5ZI2"
FT STRAND 48..51
FT /evidence="ECO:0007829|PDB:5ZI2"
FT STRAND 53..57
FT /evidence="ECO:0007829|PDB:5ZI2"
FT HELIX 62..66
FT /evidence="ECO:0007829|PDB:5ZI2"
FT STRAND 70..74
FT /evidence="ECO:0007829|PDB:5ZI2"
FT HELIX 86..107
FT /evidence="ECO:0007829|PDB:5ZI2"
FT STRAND 112..115
FT /evidence="ECO:0007829|PDB:5ZI2"
FT HELIX 120..133
FT /evidence="ECO:0007829|PDB:5ZI2"
FT HELIX 139..141
FT /evidence="ECO:0007829|PDB:5ZI2"
FT STRAND 142..144
FT /evidence="ECO:0007829|PDB:5ZI2"
FT HELIX 147..164
FT /evidence="ECO:0007829|PDB:5ZI2"
FT HELIX 166..170
FT /evidence="ECO:0007829|PDB:5ZI2"
FT HELIX 174..179
FT /evidence="ECO:0007829|PDB:5ZI2"
FT STRAND 181..185
FT /evidence="ECO:0007829|PDB:5ZI2"
FT HELIX 189..191
FT /evidence="ECO:0007829|PDB:5ZI2"
FT STRAND 192..196
FT /evidence="ECO:0007829|PDB:5ZI2"
FT HELIX 199..205
FT /evidence="ECO:0007829|PDB:5ZI2"
FT HELIX 206..208
FT /evidence="ECO:0007829|PDB:5ZI2"
FT HELIX 209..217
FT /evidence="ECO:0007829|PDB:5ZI2"
FT HELIX 219..226
FT /evidence="ECO:0007829|PDB:5ZI2"
FT TURN 227..229
FT /evidence="ECO:0007829|PDB:5ZI2"
FT HELIX 235..250
FT /evidence="ECO:0007829|PDB:5ZI2"
FT HELIX 251..253
FT /evidence="ECO:0007829|PDB:5ZI2"
FT STRAND 263..267
FT /evidence="ECO:0007829|PDB:5ZI2"
FT HELIX 268..270
FT /evidence="ECO:0007829|PDB:5ZI2"
FT HELIX 274..280
FT /evidence="ECO:0007829|PDB:5ZI2"
FT STRAND 288..296
FT /evidence="ECO:0007829|PDB:5ZI2"
FT STRAND 299..303
FT /evidence="ECO:0007829|PDB:5ZI2"
FT HELIX 306..309
FT /evidence="ECO:0007829|PDB:5ZI2"
FT HELIX 313..338
FT /evidence="ECO:0007829|PDB:5ZI2"
SQ SEQUENCE 343 AA; 37186 MW; 54725114B2CAD6A5 CRC64;
MVKVAILGAS GGVGQPLSLL LKLSPYVSEL ALYDIRAAEG IGKDLSHINT NSSCVGYDKD
SIENTLSNAQ VVLIPAGVPR KPGLTRDDLF KMNAGIVKSL VTAVGKFAPN ARILVISNPV
NSLVPIAVET LKKMGKFKPG NVMGVTNLDL VRAETFLVDY LMLKNPKIGQ EQDKTTMHRK
VTVIGGHSGE TIIPIITDKS LVFQLDKQYE HFIHRVQFGG DEIVKAKQGA GSATLSMAFA
GAKFAEEVLR SFHNEKPETE SLSAFVYLPG LKNGKKAQQL VGDNSIEYFS LPIVLRNGSV
VSIDTSVLEK LSPREEQLVN TAVKELRKNI EKGKSFILDS SKL
