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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: 4 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. Catalytic efficiency for malate oxidation is 3-fold higher with NADP.1 Publication

Catalytic activityi

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

Kineticsi

kcat is 2.6 sec(-1) for NAD-dependent malate oxidation. kcat is 1.4 sec(-1) for NADP-dependent malate oxidation.1 Publication

Manual assertion based on experiment ini

  1. KM=0.12 mM for S-malate (in the presence of NAD)1 Publication
  2. KM=0.019 mM for S-malate (in the presence of NADP)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=0.2 mM for (2S,3R)-tartrate (in the presence of NAD)1 Publication
  6. KM=5.8 mM for (2S,3R)-tartrate (in the presence of NADP)1 Publication
  7. KM=0.87 mM for NAD (in the presence of malate)1 Publication
  8. KM=0.0076 mM for NADP (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)DescriptionActionsGraphical viewLength
    Binding sitei79SubstrateBy similarity1
    Binding sitei85SubstrateBy similarity1
    Binding sitei92NADPBy similarity1
    Binding sitei117SubstrateBy similarity1
    Binding sitei148SubstrateBy similarity1
    Active sitei172Proton acceptorBy similarity1

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Nucleotide bindingi6 – 11NADPBy similarity6
    Nucleotide bindingi115 – 117NADPBy similarity3

    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

    BRENDAi1.1.1.82. 171.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Malate dehydrogenase1 Publication (EC:1.1.1.2991 Publication)
    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
    Proteomesi
    • UP000002518 Componenti: Chromosome

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00001134791 – 308Malate dehydrogenaseAdd BLAST308

    Interactioni

    Subunit structurei

    Homotetramer.1 Publication

    Protein-protein interaction databases

    STRINGi272557.APE_0672.1.

    Structurei

    Secondary structure

    1308
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi2 – 5Combined sources4
    Helixi9 – 21Combined sources13
    Beta strandi26 – 29Combined sources4
    Beta strandi31 – 34Combined sources4
    Helixi35 – 50Combined sources16
    Beta strandi56 – 60Combined sources5
    Helixi62 – 65Combined sources4
    Beta strandi69 – 73Combined sources5
    Helixi89 – 106Combined sources18
    Beta strandi111 – 114Combined sources4
    Beta strandi116 – 118Combined sources3
    Helixi119 – 130Combined sources12
    Helixi134 – 136Combined sources3
    Beta strandi137 – 139Combined sources3
    Helixi142 – 157Combined sources16
    Helixi161 – 163Combined sources3
    Beta strandi164 – 170Combined sources7
    Beta strandi177 – 185Combined sources9
    Helixi190 – 193Combined sources4
    Helixi196 – 207Combined sources12
    Helixi209 – 217Combined sources9
    Helixi223 – 237Combined sources15
    Beta strandi242 – 252Combined sources11
    Helixi253 – 255Combined sources3
    Beta strandi257 – 268Combined sources12
    Beta strandi271 – 275Combined sources5
    Helixi282 – 300Combined sources19
    Helixi304 – 307Combined sources4

    3D structure databases

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

    Miscellaneous databases

    EvolutionaryTraceiQ9YEA1.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the LDH/MDH superfamily.Curated

    Phylogenomic databases

    eggNOGiarCOG00246. Archaea.
    COG0039. LUCA.
    HOGENOMiHOG000213794.
    KOiK00024.

    Family and domain databases

    Gene3Di3.40.50.720. 1 hit.
    3.90.110.10. 1 hit.
    InterProiIPR001557. L-lactate/malate_DH.
    IPR022383. Lactate/malate_DH_C.
    IPR001236. Lactate/malate_DH_N.
    IPR015955. Lactate_DH/Glyco_Ohase_4_C.
    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.
    SUPFAMiSSF51735. SSF51735. 1 hit.
    SSF56327. 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.

    Genome annotation databases

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

    Cross-referencesi

    Sequence databases

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

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    2D4AX-ray2.87A/B/C/D1-308[»]
    ProteinModelPortaliQ9YEA1.
    SMRiQ9YEA1.
    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.
    KEGGiape:APE_0672.1.

    Phylogenomic databases

    eggNOGiarCOG00246. Archaea.
    COG0039. LUCA.
    HOGENOMiHOG000213794.
    KOiK00024.

    Enzyme and pathway databases

    BRENDAi1.1.1.82. 171.

    Miscellaneous databases

    EvolutionaryTraceiQ9YEA1.

    Family and domain databases

    Gene3Di3.40.50.720. 1 hit.
    3.90.110.10. 1 hit.
    InterProiIPR001557. L-lactate/malate_DH.
    IPR022383. Lactate/malate_DH_C.
    IPR001236. Lactate/malate_DH_N.
    IPR015955. Lactate_DH/Glyco_Ohase_4_C.
    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.
    SUPFAMiSSF51735. SSF51735. 1 hit.
    SSF56327. SSF56327. 1 hit.
    ProtoNetiSearch...

    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: November 30, 2016
    This is version 117 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Ala at position 30 is responsible for coenzyme specificity. Asp or Glu is present at this position in most NAD-specific enzymes. The next residue, Arg, is important for NADP binding.1 Publication

    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

    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 one 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.