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Q9YEA1

- MDH_AERPE

UniProt

Q9YEA1 - MDH_AERPE

Protein

Malate dehydrogenase

Gene

mdh

Organism
Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 100 (01 Oct 2014)
      Sequence version 2 (26 Jun 2007)
      Previous versions | rss
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    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

    1. L-malate dehydrogenase activity Source: UniProtKB-HAMAP
    2. malate dehydrogenase (NADP+) activity Source: UniProtKB-EC

    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, NADP

    Enzyme and pathway databases

    BioCyciAPER272557:GJD6-489-MONOMER.

    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: Chromosome

    Subcellular locationi

    Cytoplasm By similarity

    GO - Cellular componenti

    1. cytoplasm Source: UniProtKB-SubCell

    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 – 54
    Helixi9 – 2113
    Beta strandi26 – 294
    Beta strandi31 – 344
    Helixi35 – 5016
    Beta strandi56 – 605
    Helixi62 – 654
    Beta strandi69 – 735
    Helixi89 – 10618
    Beta strandi111 – 1144
    Beta strandi116 – 1183
    Helixi119 – 13012
    Helixi134 – 1363
    Beta strandi137 – 1393
    Helixi142 – 15716
    Helixi161 – 1633
    Beta strandi164 – 1707
    Beta strandi177 – 1859
    Helixi190 – 1934
    Helixi196 – 20712
    Helixi209 – 2179
    Helixi223 – 23715
    Beta strandi242 – 25211
    Helixi253 – 2553
    Beta strandi257 – 26812
    Beta strandi271 – 2755
    Helixi282 – 30019
    Helixi304 – 3074

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    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

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    MITILGAGKV GMATAVMLMM RGYDDLLLIA RTPGKPQGEA LDLAHAAAEL    50
    GVDIRISGSN SYEDMRGSDI VLVTAGIGRK PGMTREQLLE ANANTMADLA 100
    EKIKAYAKDA IVVITTNPVD AMTYVMYKKT GFPRERVIGF SGILDSARMA 150
    YYISQKLGVS FKSVNAIVLG MHGQKMFPVP RLSSVGGVPL EHLMSKEEIE 200
    EVVSETVNAG AKITELRGYS SNYGPAAGLV LTVEAIKRDS KRIYPYSLYL 250
    QGEYGYNDIV AEVPAVIGKS GIERIIELPL TEDEKRKFDE AVQAVKKLVE 300
    TLPPQLRE 308
    Length:308
    Mass (Da):33,490
    Last modified:June 26, 2007 - v2
    Checksum:iC2A14F224650B8CE
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    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:
    EMBL
    GenBank
    DDBJ
    Links Updated
    BA000002 Genomic DNA. Translation: BAA79645.2 .
    PIRi E72655.
    RefSeqi NP_147405.2. NC_000854.2.
    WP_010865893.1. NC_000854.2.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    2D4A X-ray 2.87 A/B/C/D 1-308 [» ]
    ProteinModelPortali Q9YEA1.
    SMRi Q9YEA1. Positions 1-308.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 272557.APE_0672.1.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai BAA79645 ; BAA79645 ; APE_0672.1 .
    GeneIDi 1444806.
    KEGGi ape:APE_0672.1.

    Phylogenomic databases

    eggNOGi COG0039.
    HOGENOMi HOG000213794.
    KOi K00024.

    Enzyme and pathway databases

    BioCyci APER272557:GJD6-489-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei Q9YEA1.

    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. 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: October 1, 2014
    This is version 100 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