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Entry version 133 (07 Apr 2021)
Sequence version 2 (26 Jun 2007)
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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

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the 'correct annotation' for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the 'protein existence' evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>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

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

<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section describes the catalytic activity of an enzyme, i.e. a chemical reaction that the enzyme catalyzes.<p><a href='/help/catalytic_activity' target='_top'>More...</a></p>Catalytic activityi

<p>This subsection of the 'Function' section describes biophysical and chemical properties, such as maximal absorption, kinetic parameters, pH dependence, redox potentials and temperature dependence.<p><a href='/help/biophysicochemical_properties' target='_top'>More...</a></p>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
  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
    <p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section describes the interaction between a single amino acid and another chemical entity. Priority is given to the annotation of physiological ligands.<p><a href='/help/binding' target='_top'>More...</a></p>Binding sitei79SubstrateBy similarity1
    Binding sitei85SubstrateBy similarity1
    Binding sitei92NADPBy similarity1
    Binding sitei117SubstrateBy similarity1
    Binding sitei148SubstrateBy similarity1
    <p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section is used for enzymes and indicates the residues directly involved in catalysis.<p><a href='/help/act_site' target='_top'>More...</a></p>Active sitei172Proton acceptorBy similarity1

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section describes a region in the protein which binds nucleotide phosphates. It always involves more than one amino acid and includes all residues involved in nucleotide-binding.<p><a href='/help/np_bind' target='_top'>More...</a></p>Nucleotide bindingi6 – 11NADPBy similarity6
    Nucleotide bindingi115 – 117NADPBy similarity3

    <p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

    GO - Biological processi

    <p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

    Molecular functionOxidoreductase
    Biological processTricarboxylic acid cycle
    LigandNAD, NADP

    Enzyme and pathway databases

    BRENDA Comprehensive Enzyme Information System

    More...
    BRENDAi
    1.1.1.82, 171

    <p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

    <p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>Protein namesi
    Recommended name:
    Malate dehydrogenase1 Publication (EC:1.1.1.2991 Publication)
    <p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: 'Name', 'Synonyms', 'Ordered locus names' and 'ORF names'.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
    Name:mdh
    Ordered Locus Names:APE_0672.1
    <p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiAeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1)
    <p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the 'taxonomic identifier' or 'taxid'.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri272557 [NCBI]
    <p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiArchaeaCrenarchaeotaThermoproteiDesulfurococcalesDesulfurococcaceaeAeropyrum
    <p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
    • UP000002518 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes%5Fmanual">proteome</a> can consist of several components.<br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Chromosome

    <p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the 'PTM / Processing' section describes the extent of a polypeptide chain in the mature protein following processing or proteolytic cleavage.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00001134791 – 308Malate dehydrogenaseAdd BLAST308

    <p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

    <p>This subsection of the <a href="http://www.uniprot.org/help/interaction%5Fsection">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function%5Fsection">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

    Homotetramer.

    1 Publication

    Protein-protein interaction databases

    STRING: functional protein association networks

    More...
    STRINGi
    272557.APE_0672.1

    <p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

    Secondary structure

    1308
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details

    3D structure databases

    SWISS-MODEL Repository - a database of annotated 3D protein structure models

    More...
    SMRi
    Q9YEA1

    Database of comparative protein structure models

    More...
    ModBasei
    Search...

    Protein Data Bank in Europe - Knowledge Base

    More...
    PDBe-KBi
    Search...

    Miscellaneous databases

    Relative evolutionary importance of amino acids within a protein sequence

    More...
    EvolutionaryTracei
    Q9YEA1

    <p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

    <p>This subsection of the 'Family and domains' section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

    Belongs to the LDH/MDH superfamily.Curated

    Phylogenomic databases

    evolutionary genealogy of genes: Non-supervised Orthologous Groups

    More...
    eggNOGi
    arCOG00246, Archaea

    Family and domain databases

    Conserved Domains Database

    More...
    CDDi
    cd01339, LDH-like_MDH, 1 hit

    Gene3D Structural and Functional Annotation of Protein Families

    More...
    Gene3Di
    3.90.110.10, 1 hit

    Integrated resource of protein families, domains and functional sites

    More...
    InterProi
    View protein in InterPro
    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
    IPR036291, NAD(P)-bd_dom_sf

    Pfam protein domain database

    More...
    Pfami
    View protein in Pfam
    PF02866, Ldh_1_C, 1 hit
    PF00056, Ldh_1_N, 1 hit

    PIRSF; a whole-protein classification database

    More...
    PIRSFi
    PIRSF000102, Lac_mal_DH, 1 hit

    Protein Motif fingerprint database; a protein domain database

    More...
    PRINTSi
    PR00086, LLDHDRGNASE

    Superfamily database of structural and functional annotation

    More...
    SUPFAMi
    SSF51735, SSF51735, 1 hit
    SSF56327, SSF56327, 1 hit

    <p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence%5Flength">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

    <p>This subsection of the <a href="http://www.uniprot.org/help/sequences%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>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
    <p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:iC2A14F224650B8CE
    GO

    Sequence databases

    Select the link destinations:

    EMBL nucleotide sequence database

    More...
    EMBLi

    GenBank nucleotide sequence database

    More...
    GenBanki

    DNA Data Bank of Japan; a nucleotide sequence database

    More...
    DDBJi
    Links Updated
    BA000002 Genomic DNA Translation: BAA79645.2

    Protein sequence database of the Protein Information Resource

    More...
    PIRi
    E72655

    Genome annotation databases

    Ensembl bacterial and archaeal genome annotation project

    More...
    EnsemblBacteriai
    BAA79645; BAA79645; APE_0672.1

    KEGG: Kyoto Encyclopedia of Genes and Genomes

    More...
    KEGGi
    ape:APE_0672.1

    Pathosystems Resource Integration Center (PATRIC)

    More...
    PATRICi
    fig|272557.25.peg.482

    <p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

    <p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>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:

    Protein Data Bank Europe

    More...
    PDBei

    Protein Data Bank RCSB

    More...
    RCSB PDBi

    Protein Data Bank Japan

    More...
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    2D4AX-ray2.87A/B/C/D1-308[»]
    SMRiQ9YEA1
    ModBaseiSearch...
    PDBe-KBiSearch...

    Protein-protein interaction databases

    STRINGi272557.APE_0672.1

    Genome annotation databases

    EnsemblBacteriaiBAA79645; BAA79645; APE_0672.1
    KEGGiape:APE_0672.1
    PATRICifig|272557.25.peg.482

    Phylogenomic databases

    eggNOGiarCOG00246, Archaea

    Enzyme and pathway databases

    BRENDAi1.1.1.82, 171

    Miscellaneous databases

    EvolutionaryTraceiQ9YEA1

    Family and domain databases

    CDDicd01339, LDH-like_MDH, 1 hit
    Gene3Di3.90.110.10, 1 hit
    InterProiView protein in InterPro
    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
    IPR036291, NAD(P)-bd_dom_sf
    PfamiView protein in Pfam
    PF02866, Ldh_1_C, 1 hit
    PF00056, Ldh_1_N, 1 hit
    PIRSFiPIRSF000102, Lac_mal_DH, 1 hit
    PRINTSiPR00086, LLDHDRGNASE
    SUPFAMiSSF51735, SSF51735, 1 hit
    SSF56327, SSF56327, 1 hit

    ProtoNet; Automatic hierarchical classification of proteins

    More...
    ProtoNeti
    Search...

    MobiDB: a database of protein disorder and mobility annotations

    More...
    MobiDBi
    Search...

    <p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

    <p>This subsection of the 'Entry information' section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiMDH_AERPE
    <p>This subsection of the 'Entry information' section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called 'Primary (citable) accession number'.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: Q9YEA1
    <p>This subsection of the 'Entry information' section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification ('Last modified'). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: May 30, 2000
    Last sequence update: June 26, 2007
    Last modified: April 7, 2021
    This is version 133 of the entry and version 2 of the sequence. See complete history.
    <p>This subsection of the 'Entry information' section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    <p>This section contains any relevant information that doesn't fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

    Keywords - Technical termi

    3D-structure, Reference proteome

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. SIMILARITY comments
      Index of protein domains and families
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