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Q07841

- MDH_HALMA

UniProt

Q07841 - MDH_HALMA

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Protein

Malate dehydrogenase

Gene

mdh

Organism
Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809) (Halobacterium marismortui)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli

Functioni

Catalyzes the reversible oxidation of malate to oxaloacetate.1 Publication

Catalytic activityi

(S)-malate + NAD+ = oxaloacetate + NADH.1 Publication

Kineticsi

kcat is 197 sec(-1) with oxaloacetate as substrate (in the presence of 2 M NaCl). kcat is 69 sec(-1) with oxaloacetate as substrate (in the presence of 4 M NaCl).

  1. KM=0.9 mM for oxaloacetate (in the presence of 2 M NaCl)1 Publication
  2. KM=0.7 mM for oxaloacetate (in the presence of 4 M NaCl)1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei34 – 341NAD1 Publication
Binding sitei83 – 831SubstrateBy similarity
Binding sitei89 – 891SubstrateBy similarity
Binding sitei96 – 961NAD1 Publication
Binding sitei121 – 1211SubstrateBy similarity
Binding sitei152 – 1521SubstrateBy similarity
Active sitei176 – 1761Proton acceptorBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi8 – 147NAD1 Publication
Nucleotide bindingi119 – 1213NAD1 Publication

GO - Molecular functioni

  1. L-malate dehydrogenase activity Source: UniProtKB-HAMAP

GO - Biological processi

  1. cellular carbohydrate metabolic process Source: InterPro
  2. malate metabolic process Source: InterPro
  3. tricarboxylic acid cycle Source: UniProtKB-HAMAP
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Tricarboxylic acid cycle

Keywords - Ligandi

NAD

Enzyme and pathway databases

BioCyciHMAR272569:GJDH-2431-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Malate dehydrogenase (EC:1.1.1.37)
Gene namesi
Name:mdh
Ordered Locus Names:rrnAC2706
OrganismiHaloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809) (Halobacterium marismortui)
Taxonomic identifieri272569 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaHalobacteriaHalobacterialesHalobacteriaceaeHaloarcula
ProteomesiUP000001169: Chromosome I

Subcellular locationi

Cytoplasm 1 Publication

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB-KW
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi83 – 831R → Q: Substrate specificity changes from oxaloacetate to pyruvate. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 304304Malate dehydrogenasePRO_0000113481Add
BLAST

Interactioni

Subunit structurei

Homotetramer; arranged as a dimer of dimers.3 Publications

Protein-protein interaction databases

STRINGi272569.rrnAC2706.

Structurei

Secondary structure

1
304
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi3 – 75Combined sources
Turni8 – 103Combined sources
Helixi12 – 2312Combined sources
Beta strandi28 – 336Combined sources
Helixi36 – 383Combined sources
Helixi39 – 5315Combined sources
Turni54 – 563Combined sources
Beta strandi60 – 634Combined sources
Helixi66 – 694Combined sources
Beta strandi73 – 775Combined sources
Helixi89 – 10820Combined sources
Beta strandi115 – 1184Combined sources
Helixi123 – 13311Combined sources
Beta strandi134 – 1363Combined sources
Helixi138 – 1403Combined sources
Beta strandi141 – 1433Combined sources
Helixi146 – 16116Combined sources
Helixi165 – 1673Combined sources
Beta strandi172 – 1743Combined sources
Beta strandi180 – 1823Combined sources
Helixi184 – 1863Combined sources
Helixi198 – 21619Combined sources
Turni217 – 2193Combined sources
Helixi224 – 23815Combined sources
Beta strandi244 – 25310Combined sources
Helixi254 – 2563Combined sources
Beta strandi258 – 26912Combined sources
Beta strandi272 – 2765Combined sources
Helixi283 – 30321Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1D3AX-ray2.94A/B2-304[»]
1HLPX-ray3.20A/B2-304[»]
1O6ZX-ray1.95A/B/C/D2-304[»]
2HLPX-ray2.59A/B2-304[»]
2J5KX-ray2.00A/B/C/D1-304[»]
2J5QX-ray2.15A/B/C/D1-304[»]
2J5RX-ray2.25A/B/C/D1-304[»]
2X0RX-ray2.92A/B1-304[»]
4JCOX-ray1.70A/B/C/D1-304[»]
ProteinModelPortaliQ07841.
SMRiQ07841. Positions 2-304.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ07841.

Family & Domainsi

Sequence similaritiesi

Belongs to the LDH/MDH superfamily. MDH type 3 family.Curated

Phylogenomic databases

eggNOGiCOG0039.
HOGENOMiHOG000213793.
KOiK00024.
OMAiCTADESK.

Family and domain databases

Gene3Di3.40.50.720. 1 hit.
3.90.110.10. 1 hit.
HAMAPiMF_00487. Malate_dehydrog_3.
InterProiIPR001557. 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]
PANTHERiPTHR11540. PTHR11540. 1 hit.
PfamiPF02866. Ldh_1_C. 1 hit.
PF00056. Ldh_1_N. 1 hit.
[Graphical view]
PIRSFiPIRSF000102. Lac_mal_DH. 1 hit.
PRINTSiPR00086. LLDHDRGNASE.
SUPFAMiSSF56327. SSF56327. 1 hit.

Sequencei

Sequence statusi: Complete.

Q07841-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MTKVSVVGAA GTVGAAAGYN IALRDIADEV VFVDIPDKED DTVGQAADTN
60 70 80 90 100
HGIAYDSNTR VRQGGYEDTA GSDVVVITAG IPRQPGQTRI DLAGDNAPIM
110 120 130 140 150
EDIQSSLDEH NDDYISLTTS NPVDLLNRHL YEAGDRSREQ VIGFGGRLDS
160 170 180 190 200
ARFRYVLSEE FDAPVQNVEG TILGEHGDAQ VPVFSKVRVD GTDPEFSGDE
210 220 230 240 250
KEQLLGDLQE SAMDVIERKG ATEWGPARGV AHMVEAILHD TGEVLPASVK
260 270 280 290 300
LEGEFGHEDT AFGVPVRLGS NGVEEIVEWD LDDYEQDLMA DAAEKLSDQY

DKIS
Length:304
Mass (Da):32,808
Last modified:October 1, 1994 - v1
Checksum:i0B5B630158CAD083
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti19 – 191Y → T AA sequence (PubMed:8476859)Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M97218 Genomic DNA. Translation: AAA73368.1.
AY596297 Genomic DNA. Translation: AAV47474.1.
PIRiA49496.
RefSeqiYP_137180.1. NC_006396.1.

Genome annotation databases

EnsemblBacteriaiAAV47474; AAV47474; rrnAC2706.
GeneIDi3128541.
KEGGihma:rrnAC2706.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M97218 Genomic DNA. Translation: AAA73368.1 .
AY596297 Genomic DNA. Translation: AAV47474.1 .
PIRi A49496.
RefSeqi YP_137180.1. NC_006396.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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 [» ]
4JCO X-ray 1.70 A/B/C/D 1-304 [» ]
ProteinModelPortali Q07841.
SMRi Q07841. Positions 2-304.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 272569.rrnAC2706.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAV47474 ; AAV47474 ; rrnAC2706 .
GeneIDi 3128541.
KEGGi hma:rrnAC2706.

Phylogenomic databases

eggNOGi COG0039.
HOGENOMi HOG000213793.
KOi K00024.
OMAi CTADESK.

Enzyme and pathway databases

BioCyci HMAR272569:GJDH-2431-MONOMER.

Miscellaneous databases

EvolutionaryTracei Q07841.

Family and domain databases

Gene3Di 3.40.50.720. 1 hit.
3.90.110.10. 1 hit.
HAMAPi MF_00487. Malate_dehydrog_3.
InterProi 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 ]
PANTHERi PTHR11540. PTHR11540. 1 hit.
Pfami PF02866. Ldh_1_C. 1 hit.
PF00056. Ldh_1_N. 1 hit.
[Graphical view ]
PIRSFi PIRSF000102. Lac_mal_DH. 1 hit.
PRINTSi PR00086. LLDHDRGNASE.
SUPFAMi SSF56327. SSF56327. 1 hit.
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  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, FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, SUBCELLULAR LOCATION, MUTAGENESIS OF ARG-83.
  2. 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.

Entry informationi

Entry nameiMDH_HALMA
AccessioniPrimary (citable) accession number: Q07841
Secondary accession number(s): Q5UZ29
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1994
Last sequence update: October 1, 1994
Last modified: November 26, 2014
This is version 123 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

The quarternary structure is stabilized by chloride ions bound between the subunits. This may be an adaptation to the halophilic environment.

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3