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Protein

Malate dehydrogenase

Gene

mdh

Organism
Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the reversible oxidation of malate to oxaloacetate. Can also oxidize tartrate. Can utilize both NAD and NADP. Has a preference for NADP.1 Publication

Catalytic activityi

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

Kineticsi

  1. KM=0.019 mM for S-malate (in the presence of NADP)1 Publication
  2. KM=0.12 mM for S-malate (in the presence of NAD)1 Publication
  3. KM=1.2 mM for (2S,3S)-tartrate (in the presence of NAD)1 Publication
  4. KM=23 mM for (2S,3S)-tartrate (in the presence of NADP)1 Publication
  5. KM=5.8 mM for (2S,3R)-tartrate (in the presence of NADP)1 Publication
  6. KM=0.2 mM for (2S,3R)-tartrate (in the presence of NAD)1 Publication
  7. KM=0.87 mM for NAD (in the presence of malate)1 Publication
  8. KM=0.0076 mM for NAD (in the presence of malate)1 Publication

    pH dependencei

    Optimum pH is 11 for malate oxidation.1 Publication

    Temperature dependencei

    Optimum temperature is 95 degrees Celsius.1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei79 – 791SubstrateBy similarity
    Binding sitei85 – 851SubstrateBy similarity
    Binding sitei92 – 921NADBy similarity
    Binding sitei117 – 1171SubstrateBy similarity
    Binding sitei148 – 1481SubstrateBy similarity
    Active sitei172 – 1721Proton acceptorBy similarity

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi6 – 116NADBy similarity
    Nucleotide bindingi115 – 1173NADBy similarity

    GO - Molecular functioni

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Biological processi

    Tricarboxylic acid cycle

    Keywords - Ligandi

    NAD, NADP

    Enzyme and pathway databases

    BioCyciAPER272557:GJD6-489-MONOMER.
    BRENDAi1.1.1.82. 171.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Malate dehydrogenase (EC:1.1.1.37, EC:1.1.1.82)
    Gene namesi
    Name:mdh
    Ordered Locus Names:APE_0672.1
    OrganismiAeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1)
    Taxonomic identifieri272557 [NCBI]
    Taxonomic lineageiArchaeaCrenarchaeotaThermoproteiDesulfurococcalesDesulfurococcaceaeAeropyrum
    ProteomesiUP000002518 Componenti: Chromosome

    Subcellular locationi

    GO - Cellular componenti

    Complete GO annotation...

    Keywords - Cellular componenti

    Cytoplasm

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 308308Malate dehydrogenasePRO_0000113479Add
    BLAST

    Interactioni

    Subunit structurei

    Homotetramer.1 Publication

    Protein-protein interaction databases

    STRINGi272557.APE_0672.1.

    Structurei

    Secondary structure

    1
    308
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi2 – 54Combined sources
    Helixi9 – 2113Combined sources
    Beta strandi26 – 294Combined sources
    Beta strandi31 – 344Combined sources
    Helixi35 – 5016Combined sources
    Beta strandi56 – 605Combined sources
    Helixi62 – 654Combined sources
    Beta strandi69 – 735Combined sources
    Helixi89 – 10618Combined sources
    Beta strandi111 – 1144Combined sources
    Beta strandi116 – 1183Combined sources
    Helixi119 – 13012Combined sources
    Helixi134 – 1363Combined sources
    Beta strandi137 – 1393Combined sources
    Helixi142 – 15716Combined sources
    Helixi161 – 1633Combined sources
    Beta strandi164 – 1707Combined sources
    Beta strandi177 – 1859Combined sources
    Helixi190 – 1934Combined sources
    Helixi196 – 20712Combined sources
    Helixi209 – 2179Combined sources
    Helixi223 – 23715Combined sources
    Beta strandi242 – 25211Combined sources
    Helixi253 – 2553Combined sources
    Beta strandi257 – 26812Combined sources
    Beta strandi271 – 2755Combined sources
    Helixi282 – 30019Combined sources
    Helixi304 – 3074Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2D4AX-ray2.87A/B/C/D1-308[»]
    ProteinModelPortaliQ9YEA1.
    SMRiQ9YEA1. Positions 1-308.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ9YEA1.

    Family & Domainsi

    Sequence similaritiesi

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

    Phylogenomic databases

    eggNOGiCOG0039.
    HOGENOMiHOG000213794.
    KOiK00024.

    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.

    Q9YEA1-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MITILGAGKV GMATAVMLMM RGYDDLLLIA RTPGKPQGEA LDLAHAAAEL
    60 70 80 90 100
    GVDIRISGSN SYEDMRGSDI VLVTAGIGRK PGMTREQLLE ANANTMADLA
    110 120 130 140 150
    EKIKAYAKDA IVVITTNPVD AMTYVMYKKT GFPRERVIGF SGILDSARMA
    160 170 180 190 200
    YYISQKLGVS FKSVNAIVLG MHGQKMFPVP RLSSVGGVPL EHLMSKEEIE
    210 220 230 240 250
    EVVSETVNAG AKITELRGYS SNYGPAAGLV LTVEAIKRDS KRIYPYSLYL
    260 270 280 290 300
    QGEYGYNDIV AEVPAVIGKS GIERIIELPL TEDEKRKFDE AVQAVKKLVE

    TLPPQLRE
    Length:308
    Mass (Da):33,490
    Last modified:June 26, 2007 - v2
    Checksum:iC2A14F224650B8CE
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    BA000002 Genomic DNA. Translation: BAA79645.2.
    PIRiE72655.
    RefSeqiNP_147405.2. NC_000854.2.
    WP_010865893.1. NC_000854.2.

    Genome annotation databases

    EnsemblBacteriaiBAA79645; BAA79645; APE_0672.1.
    GeneIDi1444806.
    KEGGiape:APE_0672.1.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    BA000002 Genomic DNA. Translation: BAA79645.2.
    PIRiE72655.
    RefSeqiNP_147405.2. NC_000854.2.
    WP_010865893.1. NC_000854.2.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2D4AX-ray2.87A/B/C/D1-308[»]
    ProteinModelPortaliQ9YEA1.
    SMRiQ9YEA1. Positions 1-308.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi272557.APE_0672.1.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiBAA79645; BAA79645; APE_0672.1.
    GeneIDi1444806.
    KEGGiape:APE_0672.1.

    Phylogenomic databases

    eggNOGiCOG0039.
    HOGENOMiHOG000213794.
    KOiK00024.

    Enzyme and pathway databases

    BioCyciAPER272557:GJD6-489-MONOMER.
    BRENDAi1.1.1.82. 171.

    Miscellaneous databases

    EvolutionaryTraceiQ9YEA1.

    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. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1.
    2. "Refolding, characterization and crystal structure of (S)-malate dehydrogenase from the hyperthermophilic archaeon Aeropyrum pernix."
      Kawakami R., Sakuraba H., Goda S., Tsuge H., Ohshima T.
      Biochim. Biophys. Acta 1794:1496-1504(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.87 ANGSTROMS), SUBUNIT, BIOPHYSICOCHEMICAL PROPERTIES, FUNCTION, CATALYTIC ACTIVITY.

    Entry informationi

    Entry nameiMDH_AERPE
    AccessioniPrimary (citable) accession number: Q9YEA1
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: May 30, 2000
    Last sequence update: June 26, 2007
    Last modified: May 27, 2015
    This is version 106 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, 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.