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Q07841

- MDH_HALMA

UniProt

Q07841 - MDH_HALMA

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Protein
Malate dehydrogenase
Gene
mdh, rrnAC2706
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.UniRule annotation

Catalytic activityi

(S)-malate + NAD+ = oxaloacetate + NADH.UniRule annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei34 – 341NAD
Binding sitei83 – 831Substrate By similarity
Binding sitei89 – 891Substrate By similarity
Binding sitei96 – 961NAD
Binding sitei121 – 1211Substrate By similarity
Binding sitei152 – 1521Substrate By similarity
Active sitei176 – 1761Proton acceptor By similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi8 – 147NADUniRule annotation
Nucleotide bindingi119 – 1213NADUniRule annotation

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 UniRule annotation

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB-SubCell
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.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 304304Malate dehydrogenaseUniRule annotation
PRO_0000113481Add
BLAST

Interactioni

Subunit structurei

Homotetramer; arranged as a dimer of dimers.3 Publications

Protein-protein interaction databases

STRINGi272569.rrnAC2706.

Structurei

Secondary structure

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

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
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.

Miscellaneous databases

EvolutionaryTraceiQ07841.

Family & Domainsi

Sequence similaritiesi

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

MTKVSVVGAA GTVGAAAGYN IALRDIADEV VFVDIPDKED DTVGQAADTN    50
HGIAYDSNTR VRQGGYEDTA GSDVVVITAG IPRQPGQTRI DLAGDNAPIM 100
EDIQSSLDEH NDDYISLTTS NPVDLLNRHL YEAGDRSREQ VIGFGGRLDS 150
ARFRYVLSEE FDAPVQNVEG TILGEHGDAQ VPVFSKVRVD GTDPEFSGDE 200
KEQLLGDLQE SAMDVIERKG ATEWGPARGV AHMVEAILHD TGEVLPASVK 250
LEGEFGHEDT AFGVPVRLGS NGVEEIVEWD LDDYEQDLMA DAAEKLSDQY 300
DKIS 304
Length:304
Mass (Da):32,808
Last modified:October 1, 1994 - v1
Checksum:i0B5B630158CAD083
GO

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti19 – 191Y → T AA sequence 1 Publication

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
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:
EMBL
GenBank
DDBJ
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:
PDBe
RCSB PDB
PDBj
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.
  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: May 14, 2014
This is version 120 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

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

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