Q07841 (MDH_HALMA) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Malate dehydrogenase
EC=1.1.1.37

Gene names

Name:	mdh
Ordered Locus Names:	rrnAC2706

Organism

Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809) (Halobacterium marismortui) [Complete proteome] [HAMAP]

Taxonomic identifier

272569 [NCBI]

Taxonomic lineage

cellular organisms › Archaea › Euryarchaeota › Halobacteria › Halobacteriales › Halobacteriaceae › Haloarcula › Haloarcula marismortui

Protein attributes

Sequence length	304 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.3 Ref.5 Ref.6
Subcellular location	Cytoplasm HAMAP-Rule MF_00487.
Miscellaneous	The quarternary structure is stabilized by chloride ions bound between the subunits. This may be an adaptation to the halophilic environment. HAMAP-Rule MF_00487
Sequence similarities	Belongs to the LDH/MDH superfamily. MDH type 3 family.

Ontologies

Keywords
Biological process	Tricarboxylic acid cycle
Cellular component	Cytoplasm
Ligand	NAD
Molecular function	Oxidoreductase
Technical term	3D-structure Complete proteome 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
Cellular_component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
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 – 304

304

Malate dehydrogenase HAMAP-Rule MF_00487

PRO_0000113481

Regions

Nucleotide binding

8 – 14

7

NAD HAMAP-Rule MF_00487

Nucleotide binding

119 – 121

3

NAD HAMAP-Rule MF_00487

Sites

Active site

176

1

Proton acceptor By similarity

Binding site

34

1

NAD

Binding site

83

1

Substrate By similarity

Binding site

89

1

Substrate By similarity

Binding site

96

1

NAD

Binding site

121

1

Substrate By similarity

Binding site

152

1

Substrate By similarity

Experimental info

Mutagenesis

83

1

R → Q: Substrate specificity changes from oxaloacetate to pyruvate.

Sequence conflict

19

1

Y → T AA sequence Ref.1

Secondary structure

1

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304

Helix Strand Turn

Details...

Beta strand

3 – 7

5

Turn

8 – 10

3

Helix

12 – 23

12

Beta strand

28 – 33

6

Helix

36 – 38

3

Helix

39 – 53

15

Turn

54 – 56

3

Beta strand

60 – 63

4

Helix

66 – 69

4

Beta strand

73 – 77

5

Helix

89 – 108

20

Beta strand

115 – 118

4

Helix

123 – 133

11

Beta strand

134 – 136

3

Helix

138 – 140

3

Beta strand

141 – 143

3

Helix

146 – 161

16

Helix

165 – 167

3

Beta strand

172 – 174

3

Beta strand

180 – 182

3

Helix

184 – 186

3

Helix

198 – 216

19

Turn

217 – 219

3

Helix

224 – 238

15

Beta strand

244 – 253

10

Helix

254 – 256

3

Beta strand

258 – 269

12

Beta strand

272 – 276

5

Helix

283 – 303

21

Sequences

	Sequence		Length	Mass (Da)
	Q07841 [UniParc]. Last modified October 1, 1994. Version 1. Checksum: 0B5B630158CAD083	FASTA	304	32,808
	10 20 30 40 50 60 MTKVSVVGAA GTVGAAAGYN IALRDIADEV VFVDIPDKED DTVGQAADTN HGIAYDSNTR 70 80 90 100 110 120 VRQGGYEDTA GSDVVVITAG IPRQPGQTRI DLAGDNAPIM EDIQSSLDEH NDDYISLTTS 130 140 150 160 170 180 NPVDLLNRHL YEAGDRSREQ VIGFGGRLDS ARFRYVLSEE FDAPVQNVEG TILGEHGDAQ 190 200 210 220 230 240 VPVFSKVRVD GTDPEFSGDE KEQLLGDLQE SAMDVIERKG ATEWGPARGV AHMVEAILHD 250 260 270 280 290 300 TGEVLPASVK LEGEFGHEDT AFGVPVRLGS NGVEEIVEWD LDDYEQDLMA DAAEKLSDQY DKIS

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Cloning, sequencing, and expression in Escherichia coli of the gene coding for malate dehydrogenase of the extremely halophilic archaebacterium Haloarcula marismortui." Cendrin F., Chroboczek J., Zaccai G., Eisenberg H., Mevarech M. Biochemistry 32:4308-4313(1993) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-55.
[2]	"Genome sequence of Haloarcula marismortui: a halophilic archaeon from the Dead Sea." Baliga N.S., Bonneau R., Facciotti M.T., Pan M., Glusman G., Deutsch E.W., Shannon P., Chiu Y., Weng R.S., Gan R.R., Hung P., Date S.V., Marcotte E., Hood L., Ng W.V. Genome Res. 14:2221-2234(2004) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809.
[3]	"Insights into the molecular relationships between malate and lactate dehydrogenases: structural and biochemical properties of monomeric and dimeric intermediates of a mutant of tetrameric L-[LDH-like] malate dehydrogenase from the halophilic archaeon Haloarcula marismortui." Madern D., Ebel C., Mevarech M., Richard S.B., Pfister C., Zaccai G. Biochemistry 39:1001-1010(2000) [PubMed] [Europe PMC] [Abstract] Cited for: SUBUNIT.
[4]	"Structural features that stabilize halophilic malate-dehydrogenase from an archaebacterium." Dym O., Mevarech M., Sussman J.L. Science 267:1344-1346(1995) Cited for: X-RAY CRYSTALLOGRAPHY (3.2 ANGSTROMS).
[5]	"Halophilic adaptation: novel solvent protein interactions observed in the 2.9 and 2.6 A resolution structures of the wild type and a mutant of malate dehydrogenase from Haloarcula marismortui." Richard S.B., Madern D., Garcin E., Zaccai G. Biochemistry 39:992-1000(2000) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.59 ANGSTROMS), SUBUNIT.
[6]	"The oligomeric states of Haloarcula marismortui malate dehydrogenase are modulated by solvent components as shown by crystallographic and biochemical studies." Irimia A., Ebel C., Madern D., Richard S.B., Cosenza L.W., Zaccai G., Vellieux F.M.D. J. Mol. Biol. 326:859-873(2003) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.95 ANGSTROMS) IN COMPLEX WITH NAD, SUBUNIT.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

M97218 Genomic DNA. Translation: AAA73368.1.
AY596297 Genomic DNA. Translation: AAV47474.1.

PIR

A49496.

RefSeq

YP_137180.1. NC_006396.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1D3A	X-ray	2.94	A/B	2-304	[»]
1HLP	X-ray	3.20	A/B	2-304	[»]
1O6Z	X-ray	1.95	A/B/C/D	2-304	[»]
2HLP	X-ray	2.59	A/B	2-304	[»]
2J5K	X-ray	2.00	A/B/C/D	1-304	[»]
2J5Q	X-ray	2.15	A/B/C/D	1-304	[»]
2J5R	X-ray	2.25	A/B/C/D	1-304	[»]
2X0R	X-ray	2.92	A/B	1-304	[»]

ProteinModelPortal

Q07841.

SMR

Q07841. Positions 2-304.

ModBase

Search...

Protein-protein interaction databases

STRING

272569.rrnAC2706.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAV47474; AAV47474; rrnAC2706.

GeneID

3128541.

KEGG

hma:rrnAC2706.

Organism-specific databases

CMR

Search...

Phylogenomic databases

eggNOG

COG0039.

HOGENOM

HOG000213793.

KO

K00024.

OMA

DAMTYVM.

ProtClustDB

PRK06223.

Enzyme and pathway databases

BioCyc

HMAR272569:GJDH-2431-MONOMER.

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.

ProtoNet

Search...

Other

EvolutionaryTrace

Q07841.

Entry information

Entry name

MDH_HALMA

Accession

Primary (citable) accession number: Q07841
Secondary accession number(s): Q5UZ29

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 1, 1994
Last sequence update:	October 1, 1994
Last modified:	May 1, 2013
This is version 114 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program