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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: 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

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Biological processi

    Tricarboxylic acid cycle

    Keywords - Ligandi

    NAD

    Enzyme and pathway databases

    BioCyciHMAR272569:GJDH-2431-MONOMER.
    BRENDAi1.1.1.37. 2549.

    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 Componenti: Chromosome I

    Subcellular locationi

    • Cytoplasm 1 Publication

    GO - Cellular componenti

    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.
    OMAiQKVVGMA.

    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.
    RefSeqiWP_004959949.1. NC_006396.1.
    YP_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.
    PIRiA49496.
    RefSeqiWP_004959949.1. NC_006396.1.
    YP_137180.1. NC_006396.1.

    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...

    Protein-protein interaction databases

    STRINGi272569.rrnAC2706.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

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

    Phylogenomic databases

    eggNOGiCOG0039.
    HOGENOMiHOG000213793.
    KOiK00024.
    OMAiQKVVGMA.

    Enzyme and pathway databases

    BioCyciHMAR272569:GJDH-2431-MONOMER.
    BRENDAi1.1.1.37. 2549.

    Miscellaneous databases

    EvolutionaryTraceiQ07841.

    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.
    ProtoNetiSearch...

    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: May 27, 2015
    This is version 126 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

    Similar proteinsi

    Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
    100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
    90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
    50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.