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P10584

- MDH_THETH

UniProt

P10584 - MDH_THETH

Protein

Malate dehydrogenase

Gene

mdh

Organism
Thermus thermophilus
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 120 (01 Oct 2014)
      Sequence version 1 (01 Jul 1989)
      Previous versions | rss
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    Functioni

    Catalyzes the reversible oxidation of malate to oxaloacetate.

    Catalytic activityi

    (S)-malate + NAD+ = oxaloacetate + NADH.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei92 – 921SubstrateBy similarity
    Binding sitei98 – 981SubstrateBy similarity
    Binding sitei105 – 1051NAD
    Binding sitei112 – 1121NAD
    Binding sitei131 – 1311SubstrateBy similarity
    Binding sitei162 – 1621SubstrateBy similarity
    Active sitei187 – 1871Proton acceptorBy similarity

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi11 – 177NAD
    Nucleotide bindingi129 – 1313NAD

    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

    SABIO-RKP10584.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Malate dehydrogenase (EC:1.1.1.37)
    Gene namesi
    Name:mdh
    OrganismiThermus thermophilus
    Taxonomic identifieri274 [NCBI]
    Taxonomic lineageiBacteriaDeinococcus-ThermusDeinococciThermalesThermaceaeThermus

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 327327Malate dehydrogenasePRO_0000113400Add
    BLAST

    Interactioni

    Subunit structurei

    Homodimer.1 Publication

    Protein-protein interaction databases

    STRINGi262724.TTC0168.

    Structurei

    Secondary structure

    1
    327
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi5 – 117
    Helixi15 – 2511
    Turni26 – 305
    Beta strandi36 – 416
    Helixi44 – 463
    Helixi47 – 5812
    Turni59 – 613
    Beta strandi65 – 728
    Helixi74 – 774
    Turni78 – 803
    Beta strandi82 – 865
    Helixi98 – 11922
    Beta strandi125 – 1284
    Beta strandi130 – 1323
    Helixi133 – 14210
    Helixi149 – 1513
    Beta strandi152 – 1543
    Helixi157 – 17115
    Helixi175 – 1773
    Beta strandi182 – 1854
    Beta strandi192 – 1943
    Helixi205 – 2073
    Helixi211 – 2166
    Helixi218 – 23316
    Helixi238 – 25316
    Beta strandi262 – 2676
    Helixi271 – 2733
    Beta strandi278 – 28710
    Beta strandi290 – 2934
    Helixi301 – 32323

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1BDMX-ray1.80A/B1-327[»]
    1BMDX-ray1.90A/B1-327[»]
    1IZ9X-ray2.00A/B1-327[»]
    1WZEX-ray2.00A/B1-327[»]
    1WZIX-ray2.00A/B1-327[»]
    1Y7TX-ray1.65A/B1-327[»]
    2CVQX-ray2.08A/B1-321[»]
    4KDEX-ray1.80A/B1-327[»]
    4KDFX-ray2.36A/B/C/D1-327[»]
    ProteinModelPortaliP10584.
    SMRiP10584. Positions 1-327.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP10584.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the LDH/MDH superfamily. MDH type 2 family.Curated

    Family and domain databases

    Gene3Di3.40.50.720. 1 hit.
    3.90.110.10. 1 hit.
    HAMAPiMF_01517. Malate_dehydrog_2.
    InterProiIPR001557. L-lactate/malate_DH.
    IPR022383. Lactate/malate_DH_C.
    IPR001236. Lactate/malate_DH_N.
    IPR015955. Lactate_DH/Glyco_Ohase_4_C.
    IPR001252. Malate_DH_AS.
    IPR010945. Malate_DH_type2.
    IPR016040. NAD(P)-bd_dom.
    [Graphical view]
    PANTHERiPTHR23382. PTHR23382. 1 hit.
    PfamiPF02866. Ldh_1_C. 1 hit.
    PF00056. Ldh_1_N. 1 hit.
    [Graphical view]
    PIRSFiPIRSF000102. Lac_mal_DH. 1 hit.
    SUPFAMiSSF56327. SSF56327. 1 hit.
    TIGRFAMsiTIGR01759. MalateDH-SF1. 1 hit.
    PROSITEiPS00068. MDH. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P10584-1 [UniParc]FASTAAdd to Basket

    « Hide

    MKAPVRVAVT GAAGQIGYSL LFRIAAGEML GKDQPVILQL LEIPQAMKAL    50
    EGVVMELEDC AFPLLAGLEA TDDPKVAFKD ADYALLVGAA PRKAGMERRD 100
    LLQVNGKIFT EQGRALAEVA KKDVKVLVVG NPANTNALIA YKNAPGLNPR 150
    NFTAMTRLDH NRAKAQLAKK TGTGVDRIRR MTVWGNHSST MFPDLFHAEV 200
    DGRPALELVD MEWYEKVFIP TVAQRGAAII QARGASSAAS AANAAIEHIR 250
    DWALGTPEGD WVSMAVPSQG EYGIPEGIVY SFPVTAKDGA YRVVEGLEIN 300
    EFARKRMEIT AQELLDEMEQ VKALGLI 327
    Length:327
    Mass (Da):35,426
    Last modified:July 1, 1989 - v1
    Checksum:i31FA90DED2393DF2
    GO

    Natural variant

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Natural varianti190 – 1901T → I in strain: F428; produces a 2 to 3 times higher enzyme activity.

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    J02598 Genomic DNA. Translation: AAA27499.1.
    X54073 Genomic DNA. Translation: CAA38008.1.
    X56033 Genomic DNA. Translation: CAA39508.1.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    J02598 Genomic DNA. Translation: AAA27499.1 .
    X54073 Genomic DNA. Translation: CAA38008.1 .
    X56033 Genomic DNA. Translation: CAA39508.1 .

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1BDM X-ray 1.80 A/B 1-327 [» ]
    1BMD X-ray 1.90 A/B 1-327 [» ]
    1IZ9 X-ray 2.00 A/B 1-327 [» ]
    1WZE X-ray 2.00 A/B 1-327 [» ]
    1WZI X-ray 2.00 A/B 1-327 [» ]
    1Y7T X-ray 1.65 A/B 1-327 [» ]
    2CVQ X-ray 2.08 A/B 1-321 [» ]
    4KDE X-ray 1.80 A/B 1-327 [» ]
    4KDF X-ray 2.36 A/B/C/D 1-327 [» ]
    ProteinModelPortali P10584.
    SMRi P10584. Positions 1-327.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 262724.TTC0168.

    Chemistry

    BindingDBi P10584.
    ChEMBLi CHEMBL4255.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Enzyme and pathway databases

    SABIO-RK P10584.

    Miscellaneous databases

    EvolutionaryTracei P10584.

    Family and domain databases

    Gene3Di 3.40.50.720. 1 hit.
    3.90.110.10. 1 hit.
    HAMAPi MF_01517. Malate_dehydrog_2.
    InterProi IPR001557. L-lactate/malate_DH.
    IPR022383. Lactate/malate_DH_C.
    IPR001236. Lactate/malate_DH_N.
    IPR015955. Lactate_DH/Glyco_Ohase_4_C.
    IPR001252. Malate_DH_AS.
    IPR010945. Malate_DH_type2.
    IPR016040. NAD(P)-bd_dom.
    [Graphical view ]
    PANTHERi PTHR23382. PTHR23382. 1 hit.
    Pfami PF02866. Ldh_1_C. 1 hit.
    PF00056. Ldh_1_N. 1 hit.
    [Graphical view ]
    PIRSFi PIRSF000102. Lac_mal_DH. 1 hit.
    SUPFAMi SSF56327. SSF56327. 1 hit.
    TIGRFAMsi TIGR01759. MalateDH-SF1. 1 hit.
    PROSITEi PS00068. MDH. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Nucleotide sequence of the malate dehydrogenase gene of Thermus flavus and its mutation directing an increase in enzyme activity."
      Nishiyama M., Matsubara N., Yamamoto K., Iijima S., Uozumi T., Beppu T.
      J. Biol. Chem. 261:14178-14183(1986) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-37 AND 265-284.
      Strain: ATCC 33923 / DSM 674 / AT-62.
    2. "Characterization of an operon encoding succinyl-CoA synthetase and malate dehydrogenase from Thermus flavus AT-62 and its expression in Escherichia coli."
      Nishiyama M., Horinouchi S., Beppu T.
      Mol. Gen. Genet. 226:1-9(1991) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: ATCC 33923 / DSM 674 / AT-62.
    3. "Cloning and nucleotide sequences of the mdh and sucD genes from Thermus aquaticus B."
      Nicholls D.J., Sundaram T.K., Atkinson T., Minton N.P.
      FEMS Microbiol. Lett. 58:7-14(1990) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: B / NCIB 11247.
    4. "Determinants of protein thermostability observed in the 1.9-A crystal structure of malate dehydrogenase from the thermophilic bacterium Thermus flavus."
      Kelly C.A., Nishiyama M., Ohnishi Y., Beppu T., Birktoft J.J.
      Biochemistry 32:3913-3922(1993) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS).
      Strain: ATCC 33923 / DSM 674 / AT-62.
    5. "Crystal structure of NAD-dependent malate dehydrogenase complexed with NADP(H)."
      Tomita T., Fushinobu S., Kuzuyama T., Nishiyama M.
      Biochem. Biophys. Res. Commun. 334:613-618(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.65 ANGSTROMS) IN COMPLEX WITH NADP.
    6. "Crystal structure of malate dehydrogenase from Thermus thermophilus HB8."
      RIKEN structural genomics initiative (RSGI)
      Submitted (OCT-2002) to the PDB data bank
      Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).

    Entry informationi

    Entry nameiMDH_THETH
    AccessioniPrimary (citable) accession number: P10584
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: July 1, 1989
    Last sequence update: July 1, 1989
    Last modified: October 1, 2014
    This is version 120 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Direct protein sequencing

    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