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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)DescriptionActionsGraphical viewLength
    Binding sitei34NAD1 Publication1
    Binding sitei83SubstrateBy similarity1
    Binding sitei89SubstrateBy similarity1
    Binding sitei96NAD1 Publication1
    Binding sitei121SubstrateBy similarity1
    Binding sitei152SubstrateBy similarity1
    Active sitei176Proton acceptorBy similarity1

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Nucleotide bindingi8 – 14NAD1 Publication7
    Nucleotide bindingi119 – 121NAD1 Publication3

    GO - Molecular functioni

    GO - Biological processi

    Complete GO annotation...

    Keywordsi

    Molecular functionOxidoreductase
    Biological processTricarboxylic acid cycle
    LigandNAD

    Enzyme and pathway databases

    BRENDAi1.1.1.37. 2549.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Malate dehydrogenase1 Publication (EC:1.1.1.371 Publication)
    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
    Proteomesi
    • UP000001169 Componenti: Chromosome I

    Subcellular locationi

    • Cytoplasm 1 Publication

    GO - Cellular componenti

    Keywords - Cellular componenti

    Cytoplasm

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi83R → Q: Substrate specificity changes from oxaloacetate to pyruvate. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00001134811 – 304Malate dehydrogenaseAdd BLAST304

    Interactioni

    Subunit structurei

    Homotetramer; arranged as a dimer of dimers.3 Publications

    Protein-protein interaction databases

    STRINGi272569.rrnAC2706.

    Structurei

    Secondary structure

    1304
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi3 – 7Combined sources5
    Turni8 – 10Combined sources3
    Helixi12 – 23Combined sources12
    Beta strandi28 – 33Combined sources6
    Helixi36 – 38Combined sources3
    Helixi39 – 53Combined sources15
    Turni54 – 56Combined sources3
    Beta strandi60 – 63Combined sources4
    Helixi66 – 69Combined sources4
    Beta strandi73 – 77Combined sources5
    Helixi89 – 108Combined sources20
    Beta strandi115 – 118Combined sources4
    Helixi123 – 133Combined sources11
    Beta strandi134 – 136Combined sources3
    Helixi138 – 140Combined sources3
    Beta strandi141 – 143Combined sources3
    Helixi146 – 161Combined sources16
    Helixi165 – 167Combined sources3
    Beta strandi172 – 174Combined sources3
    Beta strandi180 – 182Combined sources3
    Helixi184 – 186Combined sources3
    Helixi198 – 216Combined sources19
    Turni217 – 219Combined sources3
    Helixi224 – 238Combined sources15
    Beta strandi244 – 253Combined sources10
    Helixi254 – 256Combined sources3
    Beta strandi258 – 269Combined sources12
    Beta strandi272 – 276Combined sources5
    Helixi283 – 303Combined sources21

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB 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.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ07841.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the LDH/MDH superfamily.Curated

    Phylogenomic databases

    eggNOGiarCOG00246. Archaea.
    COG0039. LUCA.
    HOGENOMiHOG000213793.
    KOiK00024.
    OMAiPIMEDIQ.

    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.

    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)DescriptionActionsGraphical viewLength
    Sequence conflicti19Y → T AA sequence (PubMed:8476859).Curated1

    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.

    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.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB 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.
    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

    eggNOGiarCOG00246. Archaea.
    COG0039. LUCA.
    HOGENOMiHOG000213793.
    KOiK00024.
    OMAiPIMEDIQ.

    Enzyme and pathway databases

    BRENDAi1.1.1.37. 2549.

    Miscellaneous databases

    EvolutionaryTraceiQ07841.

    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_HALMA
    AccessioniPrimary (citable) accession number: Q07841
    Secondary accession number(s): Q5UZ29
    Entry historyiIntegrated into UniProtKB/Swiss-Prot: October 1, 1994
    Last sequence update: October 1, 1994
    Last modified: November 2, 2016
    This is version 136 of the entry and version 1 of the sequence. See 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

    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.