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Q07841

- MDH_HALMA

UniProt

Q07841 - MDH_HALMA

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
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    • History
      Entry version 121 (01 Oct 2014)
      Sequence version 1 (01 Oct 1994)
      Previous versions | rss
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    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

    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-SubCell

    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 – 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.
    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

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    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

    Experimental Info

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

    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

    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: October 1, 2014
    This is version 121 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