Reviewed, UniProtKB/Swiss-Prot P32419 (MDHP_YEAST)

Names and origin

Protein names

Recommended name:
    Malate dehydrogenase, peroxisomal
    EC=1.1.1.37

Gene names

Name:	MDH3
Ordered Locus Names:	YDL078C
ORF Names:	D2468

Organism

Saccharomyces cerevisiae (Baker's yeast) [Complete proteome]

Taxonomic identifier

4932 [NCBI]

Taxonomic lineage

Eukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces

Protein attributes

Sequence length	343 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level.

General annotation (Comments)

Catalytic activity	(S)-malate + NAD+ = oxaloacetate + NADH.
Subunit structure	Homodimer.
Subcellular location	Peroxisome.
Miscellaneous	Yeast contains at least 3 malate dehydrogenase isoenzymes: a mitochondrial (MDH1), a cytoplasmic (MDH2) and a peroxisomal (MDH3). Present with 3300 molecules/cell in log phase SD medium. Ref.3
Sequence similarities	Belongs to the LDH/MDH superfamily. MDH type 1 family.

Ontologies

Keywords
Biological process	Glyoxylate bypass Tricarboxylic acid cycle
Cellular component	Peroxisome
Ligand	NAD
Molecular function	Oxidoreductase
Technical term	Complete proteome Direct protein sequencing
Gene Ontology (GO)
Biological process	NADH regeneration Traceable author statement. Source: SGD fatty acid beta-oxidation Traceable author statement. Source: SGD glycolysis Inferred from electronic annotation. Source: InterPro glyoxylate cycle Traceable author statement. Source: SGD malate metabolic process Traceable author statement. Source: SGD oxidation reduction Inferred from electronic annotation. Source: UniProtKB-KW tricarboxylic acid cycle Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	peroxisome Ref.1 Inferred from direct assay. Source: SGD
Molecular function	L-malate dehydrogenase activity Inferred from mutant phenotype. Source: SGD identical protein binding Inferred from physical interaction. Source: IntAct
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
itself		1	EBI-10598,EBI-10598
	P43582	1	EBI-10598,EBI-22766
ESS1	P22696	1	EBI-10598,EBI-6679
PRP40	P33203	1	EBI-10598,EBI-701
RSP5	P39940	1	EBI-10598,EBI-16219

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Initiator methionine	1	1	Removed Ref.1
	Chain	2 – 343	342	Malate dehydrogenase, peroxisomal		PRO_0000113342
Regions
	Nucleotide binding	8 – 14	7	NAD By similarity
	Nucleotide binding	116 – 118	3	NAD By similarity
Sites
	Active site	187	1	Proton acceptor By similarity
	Binding site	34	1	NAD By similarity
	Binding site	80	1	Substrate By similarity
	Binding site	86	1	Substrate By similarity
	Binding site	93	1	NAD By similarity
	Binding site	118	1	Substrate By similarity
	Binding site	152	1	Substrate By similarity
	Binding site	237	1	NAD By similarity
Experimental info
	Sequence conflict	240	1	A → R in AAA34767. Ref.1

Sequences

	Sequence		Length	Mass (Da)
	P32419-1 [UniParc]. Last modified January 23, 2007. Version 3. Checksum: 54725114B2CAD6A5	FASTA	343	37,186
	10 20 30 40 50 60 MVKVAILGAS GGVGQPLSLL LKLSPYVSEL ALYDIRAAEG IGKDLSHINT NSSCVGYDKD 70 80 90 100 110 120 SIENTLSNAQ VVLIPAGVPR KPGLTRDDLF KMNAGIVKSL VTAVGKFAPN ARILVISNPV 130 140 150 160 170 180 NSLVPIAVET LKKMGKFKPG NVMGVTNLDL VRAETFLVDY LMLKNPKIGQ EQDKTTMHRK 190 200 210 220 230 240 VTVIGGHSGE TIIPIITDKS LVFQLDKQYE HFIHRVQFGG DEIVKAKQGA GSATLSMAFA 250 260 270 280 290 300 GAKFAEEVLR SFHNEKPETE SLSAFVYLPG LKNGKKAQQL VGDNSIEYFS LPIVLRNGSV 310 320 330 340 VSIDTSVLEK LSPREEQLVN TAVKELRKNI EKGKSFILDS SKL

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Isolation and characterization of the yeast gene encoding the MDH3 isozyme of malate dehydrogenase." Steffan J.S., McAlister-Henn L. J. Biol. Chem. 267:24708-24715(1992) [PubMed: 1447211] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 2-16; 23-36 AND 153-167.
[2]	"The nucleotide sequence of Saccharomyces cerevisiae chromosome IV." Jacq C., Alt-Moerbe J., Andre B., Arnold W., Bahr A., Ballesta J.P.G., Bargues M., Baron L., Becker A., Biteau N., Bloecker H., Blugeon C., Boskovic J., Brandt P., Brueckner M., Buitrago M.J., Coster F., Delaveau T. , del Rey F., Dujon B., Eide L.G., Garcia-Cantalejo J.M., Goffeau A., Gomez-Peris A., Granotier C., Hanemann V., Hankeln T., Hoheisel J.D., Jaeger W., Jimenez A., Jonniaux J.-L., Kraemer C., Kuester H., Laamanen P., Legros Y., Louis E.J., Moeller-Rieker S., Monnet A., Moro M., Mueller-Auer S., Nussbaumer B., Paricio N., Paulin L., Perea J., Perez-Alonso M., Perez-Ortin J.E., Pohl T.M., Prydz H., Purnelle B., Rasmussen S.W., Remacha M.A., Revuelta J.L., Rieger M., Salom D., Saluz H.P., Saiz J.E., Saren A.-M., Schaefer M., Scharfe M., Schmidt E.R., Schneider C., Scholler P., Schwarz S., Soler-Mira A., Urrestarazu L.A., Verhasselt P., Vissers S., Voet M., Volckaert G., Wagner G., Wambutt R., Wedler E., Wedler H., Woelfl S., Harris D.E., Bowman S., Brown D., Churcher C.M., Connor R., Dedman K., Gentles S., Hamlin N., Hunt S., Jones L., McDonald S., Murphy L.D., Niblett D., Odell C., Oliver K., Rajandream M.A., Richards C., Shore L., Walsh S.V., Barrell B.G., Dietrich F.S., Mulligan J.T., Allen E., Araujo R., Aviles E., Berno A., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M., Hunicke-Smith S., Hyman R.W., Komp C., Lashkari D., Lew H., Lin D., Mosedale D., Nakahara K., Namath A., Oefner P., Oh C., Petel F.X., Roberts D., Schramm S., Schroeder M., Shogren T., Shroff N., Winant A., Yelton M.A., Botstein D., Davis R.W., Johnston M., Andrews S., Brinkman R., Cooper J., Ding H., Du Z., Favello A., Fulton L., Gattung S., Greco T., Hallsworth K., Hawkins J., Hillier L.W., Jier M., Johnson D., Johnston L., Kirsten J., Kucaba T., Langston Y., Latreille P., Le T., Mardis E., Menezes S., Miller N., Nhan M., Pauley A., Peluso D., Rifkin L., Riles L., Taich A., Trevaskis E., Vignati D., Wilcox L., Wohldman P., Vaudin M., Wilson R., Waterston R., Albermann K., Hani J., Heumann K., Kleine K., Mewes H.-W., Zollner A., Zaccaria P. Nature 387:75-78(1997) [PubMed: 9169867] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[3]	"Global analysis of protein expression in yeast." Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S. Nature 425:737-741(2003) [PubMed: 14562106] [Abstract] Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	M98763 Genomic DNA. Translation: AAA34767.1. Z74126 Genomic DNA. Translation: CAA98644.1.
PIR	DEBYMP. S67614.
RefSeq	NP_010205.1.
3D structure databases
SMR	P32419. Positions 3-338.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-6473N.
IntAct	P32419. 7 interactions.
STRING	P32419.
Proteomic databases
PeptideAtlas	P32419.
Genome annotation databases
Ensembl	YDL078C; YDL078C; YDL078C; Saccharomyces cerevisiae. [Genome view]
GeneID	851481.
KEGG	sce:YDL078C.
NMPDR	fig|4932.3.peg.945.
Organism-specific databases
CYGD	YDL078c.
SGD	S000002236. MDH3.
Phylogenomic databases
eggNOG	fuNOG05363.
HOGENOM	HBG566126.
OMA	ISAHLQP.
OrthoDB	EOG9X990B.
PhylomeDB	P32419.
Enzyme and pathway databases
BRENDA	1.1.1.37. 250.
Gene expression databases
ArrayExpress	P32419.
Genevestigator	P32419.
GermOnline	YDL078C. Saccharomyces cerevisiae.
Family and domain databases
InterPro	IPR001557. L-lactate/malate_DH. IPR001236. Lactate/malate_DH. IPR015955. Lactate_DH/Glyco_Ohase_4_C. IPR001252. Malate_DH_AS. IPR010097. Malate_DH_NAD-dep_euk/g-bac. IPR016040. NAD(P)-bd_dom. [Graphical view]
Gene3D	G3DSA:3.90.110.10. lact_mal_DH. 1 hit. G3DSA:3.40.50.720. NAD(P)-bd. 1 hit.
PANTHER	PTHR11540:SF1. MDH_euk_g_bac. 1 hit.
Pfam	PF02866. Ldh_1_C. 1 hit. PF00056. Ldh_1_N. 1 hit. [Graphical view]
PIRSF	PIRSF000102. Lac_mal_DH. 1 hit.
TIGRFAMs	TIGR01772. MDH_euk_gproteo. 1 hit.
PROSITE	PS00068. MDH. 1 hit. [Graphical view]
ProtoNet	Search...
Other Resources
NextBio	968795.

Entry information

Entry name

MDHP_YEAST

Accession

Primary (citable) accession number: P32419
Secondary accession number(s): Q12689

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 1, 1993
Last sequence update:	January 23, 2007
Last modified:	February 9, 2010
This is version 96 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

FPAP (Fungal Proteome Annotation Project)