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Protein

2-pyrone-4,6-dicarbaxylate hydrolase

Gene

ligI

Organism
Sphingomonas paucimobilis (Pseudomonas paucimobilis)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Plays an important role in the metabolism of lignin-derived aromatic compounds. Involved in the meta fission degradative pathway of protocatechuate. Catalyzes the reversible hydrolysis of 2-pyrone-4,6-dicarboxylate (PDC) to a mixture of 4-carboxy-2-hydroxymuconate (CHM) and 4-oxalomesaconate (OMA). The product of the enzymatic reaction exists in two forms depending on the pH. At pH 10, the keto form (OMA) is predominant, and at pH 6, the enol form (CHM) is predominant (PubMed:22475079).3 Publications

Catalytic activityi

2-oxo-2H-pyran-4,6-dicarboxylate + H2O = (1E)-4-oxobut-1-ene-1,2,4-tricarboxylate.3 Publications

Enzyme regulationi

Strongly inhibited by 1 mM Zn2+, Cu2+, Mn2+ and Co2+ ions. Also inhibited by pyridine-2,4-dicarboxylic acid, 5-hydroxyisophthalic acid and 5,5'-dithiobis(2-nitrobenzoic acid) (Ellman reagent).3 Publications

Kineticsi

Kcat is 342 sec(-1) and 116 sec(-1) with PDC and OMA/CHM, respectively (at pH 8.25).1 Publication

Manual assertion based on experiment ini

  1. KM=18 µM for OMA/CHM (at pH 8.25)3 Publications
  2. KM=48 µM for PDC (at pH 8.25)3 Publications
  3. KM=49 µM for CHM (at pH 7 and at 30 degrees Celsius)3 Publications
  4. KM=74 µM for PDC (at pH 8.5 and at 30 degrees Celsius)3 Publications
  5. KM=90 µM for PDC3 Publications

    pH dependencei

    Optimum pH for hydrolysis of PDC is 8.5 and optimum pH for synthesis of PDC is between 6.0 to 7.5.3 Publications

    Temperature dependencei

    Optimum temperature is 50 degrees Celsius.3 Publications

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Binding sitei47Substrate1 Publication1
    Binding sitei75Substrate1 Publication1
    Binding sitei122Substrate1 Publication1
    Binding sitei128Substrate1 Publication1
    Binding sitei154Substrate1 Publication1
    Binding sitei178Substrate1 Publication1
    Active sitei2461 Publication1
    Binding sitei251Substrate1 Publication1

    GO - Molecular functioni

    • 2-pyrone-4,6-dicarboxylate lactonase activity Source: UniProtKB

    GO - Biological processi

    • 3,4-dihydroxybenzoate catabolic process Source: UniProtKB
    Complete GO annotation...

    Keywords - Molecular functioni

    Hydrolase

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-3467.
    BRENDAi3.1.1.57. 2280.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    2-pyrone-4,6-dicarbaxylate hydrolase
    Alternative name(s):
    2-pyrone-4,6-dicarboxylate lactonohydrolase
    PDC hydrolase (EC:3.1.1.57)
    Gene namesi
    Name:ligI
    OrganismiSphingomonas paucimobilis (Pseudomonas paucimobilis)
    Taxonomic identifieri13689 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaSphingomonadalesSphingomonadaceaeSphingomonas

    Pathology & Biotechi

    Disruption phenotypei

    Cells lacking this gene show a complete loss of PDC hydrolase activity and a growth defect on vanillic acid.1 Publication

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi246D → A: Almost inactive. 1 Publication1
    Mutagenesisi246D → N: Almost inactive. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00004227831 – 2932-pyrone-4,6-dicarbaxylate hydrolaseAdd BLAST293

    Expressioni

    Inductioni

    Induced by 4-hydroxybenzoic acid.1 Publication

    Interactioni

    Subunit structurei

    Homodimer.2 Publications

    Structurei

    Secondary structure

    1293
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Helixi3 – 5Combined sources3
    Beta strandi26 – 30Combined sources5
    Turni36 – 38Combined sources3
    Helixi54 – 64Combined sources11
    Beta strandi67 – 72Combined sources6
    Helixi75 – 77Combined sources3
    Helixi82 – 90Combined sources9
    Turni91 – 93Combined sources3
    Beta strandi94 – 99Combined sources6
    Helixi107 – 115Combined sources9
    Beta strandi118 – 124Combined sources7
    Turni127 – 129Combined sources3
    Helixi135 – 142Combined sources8
    Beta strandi150 – 154Combined sources5
    Helixi157 – 159Combined sources3
    Helixi160 – 169Combined sources10
    Beta strandi174 – 176Combined sources3
    Helixi177 – 180Combined sources4
    Helixi184 – 186Combined sources3
    Helixi191 – 202Combined sources12
    Beta strandi206 – 209Combined sources4
    Helixi213 – 216Combined sources4
    Helixi224 – 236Combined sources13
    Turni237 – 239Combined sources3
    Beta strandi240 – 242Combined sources3
    Helixi259 – 264Combined sources6
    Helixi266 – 269Combined sources4
    Helixi273 – 280Combined sources8
    Helixi282 – 288Combined sources7
    Helixi290 – 292Combined sources3

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    4D8LX-ray2.00A2-293[»]
    4DI8X-ray1.81A/B2-293[»]
    4DI9X-ray1.35A2-293[»]
    4DIAX-ray2.00A2-293[»]
    ProteinModelPortaliO87170.
    SMRiO87170.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiO87170.

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni31Substrate binding1

    Sequence similaritiesi

    Belongs to the PDC hydrolase family.Curated

    Family and domain databases

    InterProiIPR006680. Amidohydro-rel.
    IPR032466. Metal_Hydrolase.
    [Graphical view]
    PfamiPF04909. Amidohydro_2. 1 hit.
    [Graphical view]
    SUPFAMiSSF51556. SSF51556. 1 hit.

    Sequencei

    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
    Checksum:i95DE7EB8449AADD5
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AB015964 Genomic DNA. Translation: BAA33799.1.
    AB073227 Genomic DNA. Translation: BAB88736.1.

    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.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    4D8LX-ray2.00A2-293[»]
    4DI8X-ray1.81A/B2-293[»]
    4DI9X-ray1.35A2-293[»]
    4DIAX-ray2.00A2-293[»]
    ProteinModelPortaliO87170.
    SMRiO87170.
    ModBaseiSearch...
    MobiDBiSearch...

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-3467.
    BRENDAi3.1.1.57. 2280.

    Miscellaneous databases

    EvolutionaryTraceiO87170.

    Family and domain databases

    InterProiIPR006680. Amidohydro-rel.
    IPR032466. Metal_Hydrolase.
    [Graphical view]
    PfamiPF04909. Amidohydro_2. 1 hit.
    [Graphical view]
    SUPFAMiSSF51556. SSF51556. 1 hit.
    ProtoNetiSearch...

    Entry informationi

    Entry nameiPDCH_SPHPI
    AccessioniPrimary (citable) accession number: O87170
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: June 26, 2013
    Last sequence update: November 1, 1998
    Last modified: November 2, 2016
    This is version 68 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    This is the first enzyme from the amidohydrolase superfamily that does not require a divalent metal ion for catalytic activity.1 Publication

    Keywords - Technical termi

    3D-structure

    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.