P10584 (MDH_THETH) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Malate dehydrogenase
EC=1.1.1.37

Gene names

Name:

mdh

Organism

Thermus thermophilus

Taxonomic identifier

274 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Deinococcus-Thermus › Deinococci › Thermales › Thermaceae › Thermus

Protein attributes

Sequence length	327 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Catalyzes the reversible oxidation of malate to oxaloacetate. HAMAP-Rule MF_01517
Catalytic activity	(S)-malate + NAD+ = oxaloacetate + NADH. HAMAP-Rule MF_01517
Subunit structure	Homodimer.
Sequence similarities	Belongs to the LDH/MDH superfamily. MDH type 2 family.

Ontologies

Keywords
Biological process	Tricarboxylic acid cycle
Ligand	NAD
Molecular function	Oxidoreductase
Technical term	3D-structure Direct protein sequencing
Gene Ontology (GO)
Biological_process	cellular carbohydrate metabolic process Inferred from electronic annotation. Source: InterPro malate metabolic process Inferred from electronic annotation. Source: InterPro tricarboxylic acid cycle Inferred from electronic annotation. Source: HAMAP
Molecular_function	L-malate dehydrogenase activity Inferred from electronic annotation. Source: HAMAP nucleotide 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 – 327

327

Malate dehydrogenase HAMAP-Rule MF_01517

PRO_0000113400

Regions

Nucleotide binding

11 – 17

7

NAD HAMAP-Rule MF_01517

Nucleotide binding

129 – 131

3

NAD HAMAP-Rule MF_01517

Sites

Active site

187

1

Proton acceptor By similarity

Binding site

92

1

Substrate By similarity

Binding site

98

1

Substrate By similarity

Binding site

105

1

NAD

Binding site

112

1

NAD

Binding site

131

1

Substrate By similarity

Binding site

162

1

Substrate By similarity

Natural variations

Natural variant

190

1

T → I in strain: F428; produces a 2 to 3 times higher enzyme activity.

Secondary structure

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327

Helix Strand Turn

Details...

Beta strand

5 – 11

7

Helix

15 – 25

11

Turn

26 – 30

5

Beta strand

36 – 41

6

Helix

44 – 46

3

Helix

47 – 58

12

Turn

59 – 61

3

Beta strand

65 – 72

8

Helix

74 – 77

4

Turn

78 – 80

3

Beta strand

82 – 86

5

Helix

98 – 119

22

Beta strand

125 – 128

4

Beta strand

130 – 132

3

Helix

133 – 142

10

Helix

149 – 151

3

Beta strand

152 – 154

3

Helix

157 – 171

15

Helix

175 – 177

3

Beta strand

182 – 185

4

Beta strand

192 – 194

3

Helix

205 – 207

3

Helix

211 – 216

6

Helix

218 – 233

16

Helix

238 – 253

16

Beta strand

262 – 267

6

Helix

271 – 273

3

Beta strand

278 – 287

10

Beta strand

290 – 293

4

Helix

301 – 323

23

Sequences

	Sequence		Length	Mass (Da)
	P10584 [UniParc]. Last modified July 1, 1989. Version 1. Checksum: 31FA90DED2393DF2	FASTA	327	35,426
	10 20 30 40 50 60 MKAPVRVAVT GAAGQIGYSL LFRIAAGEML GKDQPVILQL LEIPQAMKAL EGVVMELEDC 70 80 90 100 110 120 AFPLLAGLEA TDDPKVAFKD ADYALLVGAA PRKAGMERRD LLQVNGKIFT EQGRALAEVA 130 140 150 160 170 180 KKDVKVLVVG NPANTNALIA YKNAPGLNPR NFTAMTRLDH NRAKAQLAKK TGTGVDRIRR 190 200 210 220 230 240 MTVWGNHSST MFPDLFHAEV DGRPALELVD MEWYEKVFIP TVAQRGAAII QARGASSAAS 250 260 270 280 290 300 AANAAIEHIR DWALGTPEGD WVSMAVPSQG EYGIPEGIVY SFPVTAKDGA YRVVEGLEIN 310 320 EFARKRMEIT AQELLDEMEQ VKALGLI

References

[1]	"Nucleotide sequence of the malate dehydrogenase gene of Thermus flavus and its mutation directing an increase in enzyme activity." Nishiyama M., Matsubara N., Yamamoto K., Iijima S., Uozumi T., Beppu T. J. Biol. Chem. 261:14178-14183(1986) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-37 AND 265-284. Strain: ATCC 33923 / DSM 674 / AT-62.
[2]	"Characterization of an operon encoding succinyl-CoA synthetase and malate dehydrogenase from Thermus flavus AT-62 and its expression in Escherichia coli." Nishiyama M., Horinouchi S., Beppu T. Mol. Gen. Genet. 226:1-9(1991) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 33923 / DSM 674 / AT-62.
[3]	"Cloning and nucleotide sequences of the mdh and sucD genes from Thermus aquaticus B." Nicholls D.J., Sundaram T.K., Atkinson T., Minton N.P. FEMS Microbiol. Lett. 58:7-14(1990) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: B / NCIB 11247.
[4]	"Determinants of protein thermostability observed in the 1.9-A crystal structure of malate dehydrogenase from the thermophilic bacterium Thermus flavus." Kelly C.A., Nishiyama M., Ohnishi Y., Beppu T., Birktoft J.J. Biochemistry 32:3913-3922(1993) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS). Strain: ATCC 33923 / DSM 674 / AT-62.
[5]	"Crystal structure of NAD-dependent malate dehydrogenase complexed with NADP(H)." Tomita T., Fushinobu S., Kuzuyama T., Nishiyama M. Biochem. Biophys. Res. Commun. 334:613-618(2005) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.65 ANGSTROMS) IN COMPLEX WITH NADP.
[6]	"Crystal structure of malate dehydrogenase from Thermus thermophilus HB8." RIKEN structural genomics initiative (RSGI) Submitted (OCT-2002) to the PDB data bank Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

J02598 Genomic DNA. Translation: AAA27499.1.
X54073 Genomic DNA. Translation: CAA38008.1.
X56033 Genomic DNA. Translation: CAA39508.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1BDM	X-ray	1.80	A/B	1-327	[»]
1BMD	X-ray	1.90	A/B	1-327	[»]
1IZ9	X-ray	2.00	A/B	1-327	[»]
1WZE	X-ray	2.00	A/B	1-327	[»]
1WZI	X-ray	2.00	A/B	1-327	[»]
1Y7T	X-ray	1.65	A/B	1-327	[»]
2CVQ	X-ray	2.08	A/B	1-327	[»]

ProteinModelPortal

P10584.

SMR

P10584. Positions 1-327.

ModBase

Search...

Protein-protein interaction databases

STRING

262724.TTC0168.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Enzyme and pathway databases

SABIO-RK

P10584.

Family and domain databases

Gene3D

3.40.50.720. 1 hit.
3.90.110.10. 1 hit.

HAMAP

MF_01517. Malate_dehydrog_2.

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.
IPR010945. Malate_DH_type2.
IPR016040. NAD(P)-bd_dom.
[Graphical view]

PANTHER

PTHR23382. PTHR23382. 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

TIGR01759. MalateDH-SF1. 1 hit.

PROSITE

PS00068. MDH. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

BindingDB

P10584.

ChEMBL

CHEMBL4255.

EvolutionaryTrace

P10584.

Entry information

Entry name

MDH_THETH

Accession

Primary (citable) accession number: P10584

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 1, 1989
Last sequence update:	July 1, 1989
Last modified:	April 3, 2013
This is version 113 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program