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Entry version 79 (11 Dec 2019)
Sequence version 1 (16 Aug 2004)
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Protein

2-methylcitrate dehydratase, mitochondrial

Gene

PDH1

Organism
Yarrowia lipolytica (strain CLIB 122 / E 150) (Yeast) (Candida lipolytica)
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

Component of the methylcitrate cycle that catalyzes the dehydration of 2-methylcitrate to 2-methyl-cis-aconitate. The methylcitrate cycle is a metabolic pathway for the consumption of propionic acid.5 Publications

<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">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 <a href="http://www.uniprot.org/help/function_section">Function</a> section describes regulatory mechanisms for enzymes, transporters or microbial transcription factors, and reports the components which regulate (by activation or inhibition) the reaction.<p><a href='/help/activity_regulation' target='_top'>More...</a></p>Activity regulationi

Several bivalent metal ions, such as nickel, copper, zinc, mercury, and lead, inhibit the activity to some extent. Inhibited by structural analogs such as citrate, cis-aconitate, isocitrate, 2-methylisocitrate, tricarballylate and fluorocitrate, but not by trans-aconitate or adipate.1 Publication

<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

  1. KM=0.19 mM for 2-methylcitrate1 Publication

    pH dependencei

    Optimum pH is 6.5-7.0.1 Publication

    Temperature dependencei

    Optimum temperature is 25-40 degrees Celsius.1 Publication

    <p>This subsection of the <a href="http://www.uniprot.org/help/function_section">'Function'</a> section describes the metabolic pathway(s) associated with a protein.<p><a href='/help/pathway' target='_top'>More...</a></p>Pathwayi: propanoate degradation

    This protein is involved in the pathway propanoate degradation, which is part of Organic acid metabolism.2 Publications
    View all proteins of this organism that are known to be involved in the pathway propanoate degradation and in Organic acid metabolism.

    <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 functionLyase

    Enzyme and pathway databases

    UniPathway: a resource for the exploration and annotation of metabolic pathways

    More...
    UniPathwayi
    UPA00946

    <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_and_taxonomy_section">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:
    2-methylcitrate dehydratase, mitochondrial2 Publications (EC:4.2.1.793 Publications)
    <p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">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:PDH11 Publication
    Ordered Locus Names:YALI0F02497g
    <p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">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>OrganismiYarrowia lipolytica (strain CLIB 122 / E 150) (Yeast) (Candida lipolytica)
    <p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">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 identifieri284591 [NCBI]
    <p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">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 lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesDipodascaceaeYarrowia
    <p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">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
    • UP000001300 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes_manual">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 F

    <p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

    Extracellular region or secreted Cytosol Plasma membrane Cell wall Cytoskeleton Vacuole Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte & Seán O’Donoghue; Source: COMPARTMENTS

    Keywords - Cellular componenti

    Mitochondrion

    <p>This section provides information on the disease(s) and phenotype(s) associated with a protein.<p><a href='/help/pathology_and_biotech_section' target='_top'>More...</a></p>Pathology & Biotechi

    <p>This subsection of the ‘Pathology and Biotech’ section describes the in vivo effects caused by ablation of the gene (or one or more transcripts) coding for the protein described in the entry. This includes gene knockout and knockdown, provided experiments have been performed in the context of a whole organism or a specific tissue, and not at the single-cell level.<p><a href='/help/disruption_phenotype' target='_top'>More...</a></p>Disruption phenotypei

    Leads to lipid accumulation and increased citrate production when biodiesel-derived waste glycerol is used as substrate.1 Publication

    <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 transit peptide.<p><a href='/help/transit' target='_top'>More...</a></p>Transit peptidei1 – 37MitochondrionSequence analysisAdd BLAST37
    <p>This subsection of the ‘PTM / Processing’ section describes the extent of a polypeptide chain in the mature protein following processing.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_000043335838 – 5202-methylcitrate dehydratase, mitochondrialSequence analysisAdd BLAST483

    <p>This section provides information on the expression of a gene at the mRNA or protein level in cells or in tissues of multicellular organisms.<p><a href='/help/expression_section' target='_top'>More...</a></p>Expressioni

    <p>This subsection of the ‘Expression’ section reports the experimentally proven effects of inducers and repressors (usually chemical compounds or environmental factors) on the level of protein (or mRNA) expression (up-regulation, down-regulation, constitutive expression).<p><a href='/help/induction' target='_top'>More...</a></p>Inductioni

    Slightly repressed by glucose.1 Publication

    <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_section">'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_section">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

    Monomer.

    1 Publication

    <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

    3D structure databases

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

    More...
    SMRi
    Q6C354

    Database of comparative protein structure models

    More...
    ModBasei
    Search...

    <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 PrpD family.Curated

    Keywords - Domaini

    Transit peptide

    Phylogenomic databases

    The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

    More...
    HOGENOMi
    HOG000159916

    InParanoid: Eukaryotic Ortholog Groups

    More...
    InParanoidi
    Q6C354

    KEGG Orthology (KO)

    More...
    KOi
    K01720

    Identification of Orthologs from Complete Genome Data

    More...
    OMAi
    ECTKHLG

    Family and domain databases

    Gene3D Structural and Functional Annotation of Protein Families

    More...
    Gene3Di
    1.10.4100.10, 1 hit
    3.30.1330.120, 1 hit

    Integrated resource of protein families, domains and functional sites

    More...
    InterProi
    View protein in InterPro
    IPR012705 2Me_IsoCit_deHydtase_PrpD
    IPR036148 MmgE/PrpD_sf
    IPR042183 MmgE/PrpD_sf_1
    IPR042188 MmgE/PrpD_sf_2
    IPR005656 MmgE_PrpD

    The PANTHER Classification System

    More...
    PANTHERi
    PTHR16943 PTHR16943, 1 hit

    Pfam protein domain database

    More...
    Pfami
    View protein in Pfam
    PF03972 MmgE_PrpD, 1 hit

    Superfamily database of structural and functional annotation

    More...
    SUPFAMi
    SSF103378 SSF103378, 1 hit

    TIGRFAMs; a protein family database

    More...
    TIGRFAMsi
    TIGR02330 prpD, 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_length">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_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">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.

    <p>This subsection of the <a href="http://www.uniprot.org/help/sequences_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> displayed by default in the entry is in its mature form or if it represents the precursor.<p><a href='/help/sequence_processing' target='_top'>More...</a></p>Sequence processingi: The displayed sequence is further processed into a mature form.

    Q6C354-1 [UniParc]FASTAAdd to basket
    « Hide
            10         20         30         40         50
    MRAFRSAANF GAASNIYRKS FTPASIASNR FVSARMSSIM TDNARPNTDK
    60 70 80 90 100
    VVQDIADYIH DYKIDSSVAM ETARLCFLDT LGCGLEGLKY QQCANIVGPV
    110 120 130 140 150
    VPGTIVPNGT KVPGTDYQVD PVRGAFNIGT IIRWLDFNDC WLAAEWGHPS
    160 170 180 190 200
    DNLGGILAVA DWQTRSAKAG LEGKVFKVKD VLEGMIKAHE IQGGLAIENS
    210 220 230 240 250
    FNRVGLDHVV LVKIASTAVV SGMLGLSREQ TADAISQAFV DGQSLRTYRH
    260 270 280 290 300
    APNTMSRKSW AAGDATSRAV NLALLVKKGE GGMPSILTAK TWGFYDVLFG
    310 320 330 340 350
    GKEFKFQRPY GSYVMENVLF KISFPAEFHA QTACESAMLL HEELKKLGKT
    360 370 380 390 400
    SDDIASIKIR TQEAAMRIID KKGPLHNYAD RDHCIQYMVA IPLIHGRLTA
    410 420 430 440 450
    DDYTDEIASD PRIDALREKM ECVEDKRFSE EYHAPDKRYI GNAIEITLKD
    460 470 480 490 500
    GTVLDEIEVN YPIGHRQRRE EGTPVLLEKF ARHLRGRFPE GQVEKILAAS
    510 520
    NQDIVNMDID EYVDLYVKKD
    Length:520
    Mass (Da):57,737
    Last modified:August 16, 2004 - v1
    <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:iD1470C1F5F5DC7B5
    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
    CR382132 Genomic DNA Translation: CAG77711.1

    NCBI Reference Sequences

    More...
    RefSeqi
    XP_504908.1, XM_504908.1

    Genome annotation databases

    Ensembl fungal genome annotation project

    More...
    EnsemblFungii
    CAG77711; CAG77711; YALI0_F02497g

    Database of genes from NCBI RefSeq genomes

    More...
    GeneIDi
    2908117

    KEGG: Kyoto Encyclopedia of Genes and Genomes

    More...
    KEGGi
    yli:YALI0F02497g

    <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
    CR382132 Genomic DNA Translation: CAG77711.1
    RefSeqiXP_504908.1, XM_504908.1

    3D structure databases

    SMRiQ6C354
    ModBaseiSearch...

    Genome annotation databases

    EnsemblFungiiCAG77711; CAG77711; YALI0_F02497g
    GeneIDi2908117
    KEGGiyli:YALI0F02497g

    Phylogenomic databases

    HOGENOMiHOG000159916
    InParanoidiQ6C354
    KOiK01720
    OMAiECTKHLG

    Enzyme and pathway databases

    UniPathwayiUPA00946

    Family and domain databases

    Gene3Di1.10.4100.10, 1 hit
    3.30.1330.120, 1 hit
    InterProiView protein in InterPro
    IPR012705 2Me_IsoCit_deHydtase_PrpD
    IPR036148 MmgE/PrpD_sf
    IPR042183 MmgE/PrpD_sf_1
    IPR042188 MmgE/PrpD_sf_2
    IPR005656 MmgE_PrpD
    PANTHERiPTHR16943 PTHR16943, 1 hit
    PfamiView protein in Pfam
    PF03972 MmgE_PrpD, 1 hit
    SUPFAMiSSF103378 SSF103378, 1 hit
    TIGRFAMsiTIGR02330 prpD, 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 nameiPRPD_YARLI
    <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: Q6C354
    <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_and_isoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: June 24, 2015
    Last sequence update: August 16, 2004
    Last modified: December 11, 2019
    This is version 79 of the entry and version 1 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 programFungal 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

    Reference proteome

    Documents

    1. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    2. SIMILARITY comments
      Index of protein domains and families
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