Reviewed, UniProtKB/Swiss-Prot Q9YEA1 (MDH_AERPE)

Names and origin

Protein names

Recommended name:
    Malate dehydrogenase
    EC=1.1.1.37
    EC=1.1.1.82

Gene names

Name:	mdh
Ordered Locus Names:	APE_0672.1

Organism

Aeropyrum pernix [Complete proteome] [HAMAP]

Taxonomic identifier

56636 [NCBI]

Taxonomic lineage

Archaea › Crenarchaeota › Thermoprotei › Desulfurococcales › Desulfurococcaceae › Aeropyrum

Protein attributes

Sequence length	308 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	Catalyzes the reversible oxidation of malate to oxaloacetate. Can also oxidize tartrate. Can utilize both NAD and NADP. Has a preference for NADP. HAMAP MF_00487
Catalytic activity	(S)-malate + NAD+ = oxaloacetate + NADH. HAMAP MF_00487 (S)-malate + NADP+ = oxaloacetate + NADPH.
Subunit structure	Homotetramer. Ref.2
Subcellular location	Cytoplasm By similarity HAMAP MF_00487.
Sequence similarities	Belongs to the LDH/MDH superfamily. MDH type 3 family.
Biophysicochemical properties	Kinetic parameters: KM=0.019 mM for S-malate (in the presence of NADP) KM=0.12 mM for S-malate (in the presence of NAD) KM=1.2 mM for (2S,3S)-tartrate (in the presence of NAD) KM=23 mM for (2S,3S)-tartrate (in the presence of NADP) KM=5.8 mM for (2S,3R)-tartrate (in the presence of NADP) KM=0.2 mM for (2S,3R)-tartrate (in the presence of NAD) KM=0.87 mM for NAD (in the presence of malate) KM=0.0076 mM for NAD (in the presence of malate) pH dependence: Optimum pH is 11 for malate oxidation. Temperature dependence: Optimum temperature is 95 degrees Celsius.

Ontologies

Keywords
Biological process	Tricarboxylic acid cycle
Cellular component	Cytoplasm
Ligand	NAD NADP
Molecular function	Oxidoreductase
Technical term	3D-structure Complete proteome
Gene Ontology (GO)
Biological process	glycolysis Inferred from electronic annotation. Source: InterPro malate metabolic process Inferred from electronic annotation. Source: InterPro oxidation reduction Inferred from electronic annotation. Source: UniProtKB-KW tricarboxylic acid cycle Inferred from electronic annotation. Source: HAMAP
Cellular component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	L-malate dehydrogenase activity Inferred from electronic annotation. Source: HAMAP binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 308

308

Malate dehydrogenase HAMAP MF_00487

PRO_0000113479

Regions

Nucleotide binding

6 – 11

6

NAD By similarity

Nucleotide binding

115 – 117

3

NAD By similarity

Sites

Active site

172

1

Proton acceptor By similarity

Binding site

79

1

Substrate By similarity

Binding site

85

1

Substrate By similarity

Binding site

92

1

NAD By similarity

Binding site

117

1

Substrate By similarity

Binding site

148

1

Substrate By similarity

Secondary structure

1

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308

Helix Strand Turn

Details...

Beta strand

2 – 5

4

Helix

9 – 21

13

Beta strand

26 – 29

4

Beta strand

31 – 34

4

Helix

35 – 50

16

Beta strand

56 – 60

5

Helix

62 – 65

4

Beta strand

69 – 73

5

Helix

89 – 106

18

Beta strand

111 – 114

4

Beta strand

116 – 118

3

Helix

119 – 130

12

Helix

134 – 136

3

Beta strand

137 – 139

3

Helix

142 – 157

16

Helix

161 – 163

3

Beta strand

164 – 170

7

Beta strand

177 – 185

9

Helix

190 – 193

4

Helix

196 – 207

12

Helix

209 – 217

9

Helix

223 – 237

15

Beta strand

242 – 252

11

Helix

253 – 255

3

Beta strand

257 – 268

12

Beta strand

271 – 275

5

Helix

282 – 300

19

Helix

304 – 307

4

Sequences

	Sequence		Length	Mass (Da)
	Q9YEA1-1 [UniParc]. Last modified June 26, 2007. Version 2. Checksum: C2A14F224650B8CE	FASTA	308	33,490
	10 20 30 40 50 60 MITILGAGKV GMATAVMLMM RGYDDLLLIA RTPGKPQGEA LDLAHAAAEL GVDIRISGSN 70 80 90 100 110 120 SYEDMRGSDI VLVTAGIGRK PGMTREQLLE ANANTMADLA EKIKAYAKDA IVVITTNPVD 130 140 150 160 170 180 AMTYVMYKKT GFPRERVIGF SGILDSARMA YYISQKLGVS FKSVNAIVLG MHGQKMFPVP 190 200 210 220 230 240 RLSSVGGVPL EHLMSKEEIE EVVSETVNAG AKITELRGYS SNYGPAAGLV LTVEAIKRDS 250 260 270 280 290 300 KRIYPYSLYL QGEYGYNDIV AEVPAVIGKS GIERIIELPL TEDEKRKFDE AVQAVKKLVE TLPPQLRE

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Complete genome sequence of an aerobic hyper-thermophilic crenarchaeon, Aeropyrum pernix K1." Kawarabayasi Y., Hino Y., Horikawa H., Yamazaki S., Haikawa Y., Jin-no K., Takahashi M., Sekine M., Baba S., Ankai A., Kosugi H., Hosoyama A., Fukui S., Nagai Y., Nishijima K., Nakazawa H., Takamiya M., Masuda S. , Funahashi T., Tanaka T., Kudoh Y., Yamazaki J., Kushida N., Oguchi A., Aoki K., Kubota K., Nakamura Y., Nomura N., Sako Y., Kikuchi H. DNA Res. 6:83-101(1999) [PubMed: 10382966] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K1.
[2]	"Refolding, characterization and crystal structure of (S)-malate dehydrogenase from the hyperthermophilic archaeon Aeropyrum pernix." Kawakami R., Sakuraba H., Goda S., Tsuge H., Ohshima T. Biochim. Biophys. Acta 1794:1496-1504(2009) [PubMed: 19555779] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.87 ANGSTROMS), SUBUNIT, BIOPHYSICOCHEMICAL PROPERTIES, FUNCTION, CATALYTIC ACTIVITY.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

BA000002 Genomic DNA. Translation: BAA79645.2.

PIR

E72655.

RefSeq

NP_147405.2.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2D4A	X-ray	2.87	A/B/C/D	1-308	[»]

ModBase

Search...

Genome annotation databases

GeneID

1444806.

GenomeReviews

Gene locus APE_0672.1 in contig BA000002_GR.

KEGG

ape:APE_0672.1.

NMPDR

fig|272557.1.peg.513.

Organism-specific databases

CMR

Search...

Phylogenomic databases

HOGENOM

HBG566126.

Enzyme and pathway databases

BioCyc

APER272557:APE0672-MONOMER.

BRENDA

1.1.1.37. 256344.

Family and domain databases

HAMAP

MF_00487. Malate_dehydrog_3.
[Tree]

InterPro

IPR001557. L-lactate/malate_DH.
IPR001236. Lactate/malate_DH.
IPR015955. Lactate_DH/Glyco_Ohase_4_C.
IPR011275. Malate_DH_NAD-dep_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.

Pfam

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

PIRSF

PIRSF000102. Lac_mal_DH. 1 hit.

PRINTS

PR00086. LLDHDRGNASE.

ProtoNet

Search...

Entry information

Entry name

MDH_AERPE

Accession

Primary (citable) accession number: Q9YEA1

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 30, 2000
Last sequence update:	June 26, 2007
Last modified:	January 19, 2010
This is version 74 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)