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Entry version 83 (07 Apr 2021)
Sequence version 1 (01 Nov 1998)
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Protein

2-pyrone-4,6-dicarboxylate hydrolase

Gene

ligI

Organism
Sphingobium sp. (strain NBRC 103272 / SYK-6)
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

Contributes to the degradation of lignin at the level of the protocatechuate 4,5-cleavage pathway (PubMed:9864312). Catalyzes the hydrolysis of 2-pyrone-4,6-dicarboxylate (PDC) to (4E)-oxalomesaconate (OMA) (PubMed:29658701, PubMed:22475079). The keto form of OMA can tautomerize into the enol form, 4-carboxy-2-hydroxymuconate (CHM), under certain pH conditions (PubMed:22475079). Also catalyzes the reverse reaction (PubMed:22475079, PubMed:9864312). Is essential for the growth of Sphingobium sp. SYK-6 on vanillate but is not responsible for the growth of this strain on syringate (PubMed:9864312).3 Publications

Miscellaneous

This is the first enzyme from the amidohydrolase superfamily that does not require a divalent metal ion for catalytic activity.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 <a href="http://www.uniprot.org/help/function%5Fsection">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

Strongly inhibited by 1 mM Zn2+ ions (PubMed:9864312). Also inhibited by pyridine-2,4-dicarboxylic acid, 5-hydroxyisophthalic acid and 5,5'-dithiobis(2-nitrobenzoic acid) (Ellman reagent) (PubMed:22475079, PubMed:9864312).2 Publications

<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 342 sec(-1) for the hydrolysis of 2-pyrone-4,6-dicarboxylate (at pH 8.25). kcat is 116 sec(-1) for the synthesis of 2-pyrone-4,6-dicarboxylat from OMA/CHM (at pH 8.25).1 Publication
  1. KM=18 µM for a mixture of (4E)-oxalomesaconate/4-carboxy-2-hydroxymuconate (at pH 8.25)1 Publication
  2. KM=48 µM for 2-pyrone-4,6-dicarboxylate (at pH 8.25)1 Publication
  3. KM=49 µM for 4-carboxy-2-hydroxymuconate (at pH 7 and at 30 degrees Celsius)1 Publication
  4. KM=74 µM for 2-pyrone-4,6-dicarboxylate (at pH 8.5 and at 30 degrees Celsius)1 Publication

    pH dependencei

    Optimum pH for hydrolysis of PDC is 8.5 and optimum pH for synthesis of PDC is between 6.0 to 7.5.1 Publication

    Temperature dependencei

    Optimum temperature is 50 degrees Celsius.1 Publication

    <p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">'Function'</a> section describes the metabolic pathway(s) associated with a protein.<p><a href='/help/pathway' target='_top'>More...</a></p>Pathwayi: lignin degradation

    This protein is involved in the pathway lignin degradation, which is part of Secondary metabolite metabolism.1 Publication
    View all proteins of this organism that are known to be involved in the pathway lignin degradation and in Secondary metabolite metabolism.

    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 sitei47Substrate1 Publication1
    Binding sitei75Substrate1 Publication1
    Binding sitei122Substrate1 Publication1
    Binding sitei128Substrate1 Publication1
    Binding sitei154Substrate1 Publication1
    Binding sitei178Substrate1 Publication1
    <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 sitei246Proton acceptor1 Publication1
    Binding sitei251Substrate1 Publication1

    <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 functionHydrolase
    Biological processAromatic hydrocarbons catabolism

    Enzyme and pathway databases

    BioCyc Collection of Pathway/Genome Databases

    More...
    BioCyci
    MetaCyc:MONOMER-3467

    BRENDA Comprehensive Enzyme Information System

    More...
    BRENDAi
    3.1.1.57, 2280

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

    More...
    UniPathwayi
    UPA00892

    <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:
    2-pyrone-4,6-dicarboxylate hydrolase1 Publication (EC:3.1.1.572 Publications)
    Short name:
    PDC hydrolase1 Publication
    Alternative name(s):
    2-pyrone-4,6-dicarboxylate lactonase1 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:ligIImported
    ORF Names:SLG_12570Imported
    <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>OrganismiSphingobium sp. (strain NBRC 103272 / SYK-6)
    <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 identifieri627192 [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 lineageiBacteriaProteobacteriaAlphaproteobacteriaSphingomonadalesSphingomonadaceaeSphingobium
    <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
    • UP000001275 <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 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

    Cells lacking this gene show a complete loss of PDC hydrolase activity and a growth defect on vanillic acid. Growth on syringic acid is not affected.1 Publication

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the <a href="http://www.uniprot.org/manual/pathology%5Fand%5Fbiotech%5Fsection">'Pathology and Biotech'</a> section describes the effect of the experimental mutation of one or more amino acid(s) on the biological properties of the protein.<p><a href='/help/mutagen' target='_top'>More...</a></p>Mutagenesisi246D → A: Loss of catalytic activity. 1 Publication1
    Mutagenesisi246D → N: Almost inactive. 1 Publication1

    <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_00004227831 – 2932-pyrone-4,6-dicarboxylate hydrolaseAdd BLAST293

    <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

    Monomer.

    1 Publication

    Protein-protein interaction databases

    STRING: functional protein association networks

    More...
    STRINGi
    627192.SLG_12570

    <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

    1293
    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
    O87170

    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
    O87170

    <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

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the 'Family and Domains' section describes a region of interest that cannot be described in other subsections.<p><a href='/help/region' target='_top'>More...</a></p>Regioni29 – 31Substrate binding1 Publication3

    <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

    Phylogenomic databases

    evolutionary genealogy of genes: Non-supervised Orthologous Groups

    More...
    eggNOGi
    COG3618, Bacteria

    The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

    More...
    HOGENOMi
    CLU_064039_2_1_5

    Database of Orthologous Groups

    More...
    OrthoDBi
    1979322at2

    Family and domain databases

    Integrated resource of protein families, domains and functional sites

    More...
    InterProi
    View protein in InterPro
    IPR006680, Amidohydro-rel
    IPR032466, Metal_Hydrolase

    Pfam protein domain database

    More...
    Pfami
    View protein in Pfam
    PF04909, Amidohydro_2, 1 hit

    Superfamily database of structural and functional annotation

    More...
    SUPFAMi
    SSF51556, SSF51556, 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.

    O87170-1 [UniParc]FASTAAdd to basket
    « Hide
            10         20         30         40         50
    MTNDERILSW NETPSKPRYT PPPGAIDAHC HVFGPMAQFP FSPKAKYLPR
    60 70 80 90 100
    DAGPDMLFAL RDHLGFARNV IVQASCHGTD NAATLDAIAR AQGKARGIAV
    110 120 130 140 150
    VDPAIDEAEL AALHEGGMRG IRFNFLKRLV DDAPKDKFLE VAGRLPAGWH
    160 170 180 190 200
    VVIYFEADIL EELRPFMDAI PVPIVIDHMG RPDVRQGPDG ADMKAFRRLL
    210 220 230 240 250
    DSREDIWFKA TCPDRLDPAG PPWDDFARSV APLVADYADR VIWGTDWPHP
    260 270 280 290
    NMQDAIPDDG LVVDMIPRIA PTPELQHKML VTNPMRLYWS EEM
    Length:293
    Mass (Da):32,775
    Last modified:November 1, 1998 - 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:i95DE7EB8449AADD5
    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
    AB015964 Genomic DNA Translation: BAA33799.1
    AB073227 Genomic DNA Translation: BAB88736.1
    AP012222 Genomic DNA Translation: BAK65932.1

    NCBI Reference Sequences

    More...
    RefSeqi
    WP_014075583.1, NC_015976.1

    Genome annotation databases

    Ensembl bacterial and archaeal genome annotation project

    More...
    EnsemblBacteriai
    BAK65932; BAK65932; SLG_12570

    KEGG: Kyoto Encyclopedia of Genes and Genomes

    More...
    KEGGi
    ssy:SLG_12570

    <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
    AB015964 Genomic DNA Translation: BAA33799.1
    AB073227 Genomic DNA Translation: BAB88736.1
    AP012222 Genomic DNA Translation: BAK65932.1
    RefSeqiWP_014075583.1, NC_015976.1

    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
    4D8LX-ray2.00A2-293[»]
    4DI8X-ray1.81A/B2-293[»]
    4DI9X-ray1.35A2-293[»]
    4DIAX-ray2.00A2-293[»]
    SMRiO87170
    ModBaseiSearch...
    PDBe-KBiSearch...

    Protein-protein interaction databases

    STRINGi627192.SLG_12570

    Genome annotation databases

    EnsemblBacteriaiBAK65932; BAK65932; SLG_12570
    KEGGissy:SLG_12570

    Phylogenomic databases

    eggNOGiCOG3618, Bacteria
    HOGENOMiCLU_064039_2_1_5
    OrthoDBi1979322at2

    Enzyme and pathway databases

    UniPathwayiUPA00892
    BioCyciMetaCyc:MONOMER-3467
    BRENDAi3.1.1.57, 2280

    Miscellaneous databases

    EvolutionaryTraceiO87170

    Family and domain databases

    InterProiView protein in InterPro
    IPR006680, Amidohydro-rel
    IPR032466, Metal_Hydrolase
    PfamiView protein in Pfam
    PF04909, Amidohydro_2, 1 hit
    SUPFAMiSSF51556, SSF51556, 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 nameiLIGI_SPHSK
    <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: O87170
    Secondary accession number(s): G2IQR0
    <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: June 26, 2013
    Last sequence update: November 1, 1998
    Last modified: April 7, 2021
    This is version 83 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 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. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. SIMILARITY comments
      Index of protein domains and families
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