P0C890 (MDH_PROVB) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Malate dehydrogenase
EC=1.1.1.37

Gene names

Name:

mdh

Organism

Prosthecochloris vibrioformis (Chlorobium vibrioforme)

Taxonomic identifier

1098 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Bacteroidetes/Chlorobi group › Chlorobi › Chlorobia › Chlorobiales › Chlorobiaceae › Prosthecochloris

Protein attributes

Sequence length	310 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_00487
Catalytic activity	(S)-malate + NAD+ = oxaloacetate + NADH. HAMAP-Rule MF_00487
Subunit structure	Homotetramer; arranged as a dimer of dimers. Ref.2
Sequence similarities	Belongs to the LDH/MDH superfamily. MDH type 3 family.

Ontologies

Keywords
Biological process	Tricarboxylic acid cycle
Ligand	NAD
Molecular function	Oxidoreductase
Technical term	3D-structure
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 – 310

310

Malate dehydrogenase HAMAP-Rule MF_00487

PRO_0000113449

Regions

Nucleotide binding

7 – 12

6

NAD By similarity

Nucleotide binding

117 – 119

3

NAD By similarity

Sites

Active site

174

1

Proton acceptor By similarity

Binding site

32

1

NAD By similarity

Binding site

81

1

Substrate By similarity

Binding site

87

1

Substrate By similarity

Binding site

94

1

NAD By similarity

Binding site

119

1

Substrate By similarity

Binding site

150

1

Substrate By similarity

Secondary structure

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310

Helix Strand Turn

Details...

Beta strand

2 – 6

5

Helix

10 – 21

12

Beta strand

26 – 31

6

Beta strand

33 – 36

4

Helix

37 – 46

10

Helix

49 – 52

4

Beta strand

57 – 62

6

Helix

64 – 67

4

Beta strand

71 – 75

5

Helix

87 – 105

19

Turn

106 – 108

3

Beta strand

113 – 116

4

Helix

121 – 132

12

Helix

136 – 138

3

Beta strand

139 – 141

3

Helix

144 – 159

16

Helix

163 – 165

3

Beta strand

170 – 172

3

Helix

175 – 177

3

Beta strand

178 – 180

3

Helix

182 – 184

3

Helix

192 – 194

3

Helix

198 – 209

12

Helix

211 – 219

9

Beta strand

220 – 222

3

Helix

226 – 240

15

Beta strand

245 – 255

11

Helix

256 – 258

3

Beta strand

260 – 271

12

Beta strand

274 – 278

5

Helix

285 – 301

17

Sequences

	Sequence		Length	Mass (Da)
	P0C890 [UniParc]. Last modified October 14, 2008. Version 1. Checksum: DFF3033B27FEC714	FASTA	310	33,273
	10 20 30 40 50 60 MKITVIGAGN VGATTAFRIA DKKLARELVL LDVVEGIPQG KGLDMYETGP VGLFDTKITG 70 80 90 100 110 120 SNDYADTADS DIVIITAGLP RKPGMTREDL LMKNAGIVKE VTDNIMKHSK NPIIIVVSNP 130 140 150 160 170 180 LDIMTHVAWV RSGLPKERVI GMAGVLDAAR FRSFIAMELG VSMQDINACV LGGHGDAMVP 190 200 210 220 230 240 VVKYTTVAGI PISDLLPAET IDKLVERTRN GGAEIVEHLK QGSAFYSPGS SVVEMVESIV 250 260 270 280 290 300 LDRKRVLPCA VGLEGQYGID KTFVGVPVKL GRNGVEQIYE INLDQADLDL LQKSAKIVDE 310 NCKMLESTIG

References

[1]	"Malate dehydrogenase from the mesophile Chlorobium vibrioforme and from the mild thermophile Chlorobium tepidum: molecular cloning, construction of a hybrid, and expression in Escherichia coli." Naterstad K., Lauvrak V., Sirevag R. J. Bacteriol. 178:7047-7052(1996) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"Structural basis for thermophilic protein stability: structures of thermophilic and mesophilic malate dehydrogenases." Dalhus B., Saarinen M., Sauer U.H., Eklund P., Johansson K., Karlsson A., Ramaswamy S., Bjoerk A., Synstad B., Naterstad K., Sirevaag R., Eklund H. J. Mol. Biol. 318:707-721(2002) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS), SUBUNIT.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

X80837 Genomic DNA. Translation: CAA56809.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1GUZ	X-ray	2.00	A/B/C/D	72-310	[»]
1GV1	X-ray	2.50	A/B/C/D	1-310	[»]

ProteinModelPortal

P0C890.

SMR

P0C890. Positions 1-305.

ModBase

Search...

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Family and domain databases

Gene3D

3.40.50.720. 1 hit.
3.90.110.10. 1 hit.

HAMAP

MF_00487. Malate_dehydrog_3.

InterPro

IPR001557. L-lactate/malate_DH.
IPR022383. Lactate/malate_DH_C.
IPR001236. Lactate/malate_DH_N.
IPR015955. Lactate_DH/Glyco_Ohase_4_C.
IPR011275. Malate_DH_type3.
IPR016040. NAD(P)-bd_dom.
[Graphical view]

PANTHER

PTHR11540. PTHR11540. 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.

SUPFAM

SSF56327. Lactate_DH/Glyco_hydro_4_C. 1 hit.

TIGRFAMs

TIGR01763. MalateDH_bact. 1 hit.

ProtoNet

Search...

Other

EvolutionaryTrace

P0C890.

Entry information

Entry name

MDH_PROVB

Accession

Primary (citable) accession number: P0C890
Secondary accession number(s): P80038, P94687

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 14, 2008
Last sequence update:	October 14, 2008
Last modified:	April 3, 2013
This is version 26 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program