Malate dehydrogenase, mitochondrial precursor - Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)

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P17505 (MDHM_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 130. History...

Clusters with 100%, 90%, 50% identity |

Documents (4) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
Malate dehydrogenase, mitochondrial
EC=1.1.1.37

Gene names

Name:	MDH1
Ordered Locus Names:	YKL085W

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

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

Protein attributes

Sequence length	334 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	Mitochondrion matrix Ref.6.
Miscellaneous	Yeast contains at least 3 malate dehydrogenase isoenzymes: a mitochondrial (MDH1), a cytoplasmic (MDH2) and a peroxisomal (MDH3). Present with 28100 molecules/cell in log phase SD medium.
Sequence similarities	Belongs to the LDH/MDH superfamily. MDH type 1 family.

Ontologies

Keywords
Biological process	Tricarboxylic acid cycle
Cellular component	Mitochondrion
Domain	Transit peptide
Ligand	NAD
Molecular function	Oxidoreductase
PTM	Phosphoprotein
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	cellular carbohydrate metabolic process Inferred from electronic annotation. Source: InterPro chronological cell aging Inferred from mutant phenotype PubMed 18381895. Source: SGD malate metabolic process Inferred from electronic annotation. Source: InterPro replicative cell aging Inferred from mutant phenotype PubMed 18381895. Source: SGD tricarboxylic acid cycle Inferred from mutant phenotype PubMed 3312168. Source: SGD
Cellular_component	mitochondrial matrix Inferred from direct assay PubMed 9774331. Source: SGD
Molecular_function	L-malate dehydrogenase activity Inferred from direct assay PubMed 1898005. Source: SGD mRNA binding Inferred from direct assay PubMed 21124907. Source: SGD nucleotide binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
SSA2	P10592	2	EBI-10594,EBI-8603

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Transit peptide

1 – 17

Mitochondrion Ref.1 Ref.5

Chain

18 – 334

317

Malate dehydrogenase, mitochondrial

PRO_0000018633

Regions

Nucleotide binding

24 – 30

NAD By similarity

Nucleotide binding

135 – 137

NAD By similarity

Sites

Active site

195

Proton acceptor By similarity

Binding site

NAD By similarity

Binding site

Substrate By similarity

Binding site

105

Substrate By similarity

Binding site

112

NAD By similarity

Binding site

137

Substrate By similarity

Binding site

171

Substrate By similarity

Binding site

245

NAD By similarity

Amino acid modifications

Modified residue

177

Phosphoserine Ref.8

Experimental info

Sequence conflict

S → G AA sequence Ref.5

Sequence conflict

306

S → F in AAS56240. Ref.4

Sequences

Sequence

Length

Mass (Da)

Tools

P17505 [UniParc].

Last modified June 1, 1994. Version 2.
Checksum: 8645C4CDFB9857C8
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FASTA

334

35,650

        10         20         30         40         50         60 
MLSRVAKRAF SSTVANPYKV TVLGAGGGIG QPLSLLLKLN HKVTDLRLYD LKGAKGVATD 

        70         80         90        100        110        120 
LSHIPTNSVV KGFTPEEPDG LNNALKDTDM VLIPAGVPRK PGMTRDDLFA INASIVRDLA 

       130        140        150        160        170        180 
AATAESAPNA AILVISNPVN STVPIVAQVL KNKGVYNPKK LFGVTTLDSI RAARFISEVE 

       190        200        210        220        230        240 
NTDPTQERVN VIGGHSGITI IPLISQTNHK LMSDDKRHEL IHRIQFGGDE VVKAKNGAGS 

       250        260        270        280        290        300 
ATLSMAHAGA KFANAVLSGF KGERDVIEPS FVDSPLFKSE GIEFFASPVT LGPDGIEKIH 

       310        320        330 
PIGELSSEEE EMLQKCKETL KKNIEKGVNF VASK

« Hide

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Gene sequence and primary structure of mitochondrial malate dehydrogenase from Saccharomyces cerevisiae." Thompson L.M., Sutherland P., Steffan J.S., McAlister-Henn L. Biochemistry 27:8393-8400(1988) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 18-33. Strain: S173-6B.
[2]	"Complete DNA sequence of yeast chromosome XI." Dujon B., Alexandraki D., Andre B., Ansorge W., Baladron V., Ballesta J.P.G., Banrevi A., Bolle P.-A., Bolotin-Fukuhara M., Bossier P., Bou G., Boyer J., Buitrago M.J., Cheret G., Colleaux L., Daignan-Fornier B., del Rey F., Dion C. Mewes H.-W. Nature 369:371-378(1994) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 96604 / S288c / FY1679.
[3]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[4]	"Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiae." Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F., Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A., Raphael J., Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., Williamson J. LaBaer J. Genome Res. 17:536-543(2007) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[5]	"Purification procedure and N-terminal amino acid sequence of yeast malate dehydrogenase isoenzymes." Kopetzki E., Entian K.-D., Lottspeich F., Mecke D. Biochim. Biophys. Acta 912:398-403(1987) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 18-73.
[6]	"Yeast mitochondrial dehydrogenases are associated in a supramolecular complex." Grandier-Vazeille X., Bathany K., Chaignepain S., Camougrand N., Manon S., Schmitter J.-M. Biochemistry 40:9758-9769(2001) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 55-62, SUBCELLULAR LOCATION. Strain: ATCC 201238 / W303-1B.
[7]	"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] [Europe PMC] [Abstract] Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[8]	"Profiling phosphoproteins of yeast mitochondria reveals a role of phosphorylation in assembly of the ATP synthase." Reinders J., Wagner K., Zahedi R.P., Stojanovski D., Eyrich B., van der Laan M., Rehling P., Sickmann A., Pfanner N., Meisinger C. Mol. Cell. Proteomics 6:1896-1906(2007) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-177, MASS SPECTROMETRY. Strain: ATCC 76625 / YPH499.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

J02841 Genomic DNA. Translation: AAA34759.1.
Z28085 Genomic DNA. Translation: CAA81923.1.
AY557914 Genomic DNA. Translation: AAS56240.1.
BK006944 Genomic DNA. Translation: DAA09073.1.

PIR

DEBYMM. A31945.

RefSeq

NP_012838.1. NM_001179651.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1HR9	X-ray	3.01	O/P/Q/R	2-9	[»]

ProteinModelPortal

P17505.

SMR

P17505. Positions 19-331.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-5734N.

IntAct

P17505. 30 interactions.

MINT

MINT-697512.

STRING

4932.YKL085W.

2D gel databases

UCD-2DPAGE

P17505.

Proteomic databases

PaxDb

P17505.

PeptideAtlas

P17505.

PRIDE

P17505.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblFungi

YKL085W; YKL085W; YKL085W.

GeneID

853777.

KEGG

sce:YKL085W.

Organism-specific databases

CYGD

YKL085w.

SGD

S000001568. MDH1.

Phylogenomic databases

eggNOG

COG0039.

GeneTree

ENSGT00390000016686.

HOGENOM

HOG000213792.

K00026.

OMA

DVVDYAY.

OrthoDB

EOG4CRQ7W.

Gene expression databases

Genevestigator

P17505.

GermOnline

YKL085W. Saccharomyces cerevisiae.

Family and domain databases

Gene3D

3.40.50.720. 1 hit.
3.90.110.10. 1 hit.

InterPro

IPR001557. L-lactate/malate_DH.
IPR022383. Lactate/malate_DH_C.
IPR001236. Lactate/malate_DH_N.
IPR015955. Lactate_DH/Glyco_Ohase_4_C.
IPR001252. Malate_DH_AS.
IPR010097. Malate_DH_type1.
IPR016040. NAD(P)-bd_dom.
[Graphical view]

PANTHER

PTHR11540. PTHR11540. 1 hit.
PTHR11540:SF1. PTHR11540:SF1. 1 hit.

Pfam

PF02866. Ldh_1_C. 1 hit.
PF00056. Ldh_1_N. 1 hit.
[Graphical view]

PIRSF

PIRSF000102. Lac_mal_DH. 1 hit.

SUPFAM

SSF56327. Lactate_DH/Glyco_hydro_4_C. 1 hit.

TIGRFAMs

TIGR01772. MDH_euk_gproteo. 1 hit.

PROSITE

PS00068. MDH. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P17505.

NextBio

974888.

Entry information

Entry name

MDHM_YEAST

Accession

Primary (citable) accession number: P17505
Secondary accession number(s): D6VXK3, E9P8U0

Entry history

Integrated into UniProtKB/Swiss-Prot:	August 1, 1990
Last sequence update:	June 1, 1994
Last modified:	May 1, 2013
This is version 130 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program

Relevant documents

Yeast

Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD

Yeast chromosome XI

Yeast (Saccharomyces cerevisiae) chromosome XI: entries and gene names

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Binary interactions

With

Entry

#Exp.

IntAct

Notes

Sequence annotation (Features)

Molecule processing

Regions

Sites

Amino acid modifications

Experimental info

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

2D gel databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Gene expression databases

Family and domain databases

Other

Entry information

Relevant documents