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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

  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)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei47 – 471Substrate1 Publication
    Binding sitei75 – 751Substrate1 Publication
    Binding sitei122 – 1221Substrate1 Publication
    Binding sitei128 – 1281Substrate1 Publication
    Binding sitei154 – 1541Substrate1 Publication
    Binding sitei178 – 1781Substrate1 Publication
    Active sitei246 – 24611 Publication
    Binding sitei251 – 2511Substrate1 Publication

    GO - Molecular functioni

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

    GO - Biological processi

    • protocatechuate 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)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi246 – 2461D → A: Almost inactive. 1 Publication
    Mutagenesisi246 – 2461D → N: Almost inactive. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 2932932-pyrone-4,6-dicarbaxylate hydrolasePRO_0000422783Add
    BLAST

    Expressioni

    Inductioni

    Induced by 4-hydroxybenzoic acid.1 Publication

    Interactioni

    Subunit structurei

    Homodimer.2 Publications

    Structurei

    Secondary structure

    1
    293
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi3 – 53Combined sources
    Beta strandi26 – 305Combined sources
    Turni36 – 383Combined sources
    Helixi54 – 6411Combined sources
    Beta strandi67 – 726Combined sources
    Helixi75 – 773Combined sources
    Helixi82 – 909Combined sources
    Turni91 – 933Combined sources
    Beta strandi94 – 996Combined sources
    Helixi107 – 1159Combined sources
    Beta strandi118 – 1247Combined sources
    Turni127 – 1293Combined sources
    Helixi135 – 1428Combined sources
    Beta strandi150 – 1545Combined sources
    Helixi157 – 1593Combined sources
    Helixi160 – 16910Combined sources
    Beta strandi174 – 1763Combined sources
    Helixi177 – 1804Combined sources
    Helixi184 – 1863Combined sources
    Helixi191 – 20212Combined sources
    Beta strandi206 – 2094Combined sources
    Helixi213 – 2164Combined sources
    Helixi224 – 23613Combined sources
    Turni237 – 2393Combined sources
    Beta strandi240 – 2423Combined sources
    Helixi259 – 2646Combined sources
    Helixi266 – 2694Combined sources
    Helixi273 – 2808Combined sources
    Helixi282 – 2887Combined sources
    Helixi290 – 2923Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    4D8LX-ray2.00A2-293[»]
    4DI8X-ray1.81A/B2-293[»]
    4DI9X-ray1.35A2-293[»]
    4DIAX-ray2.00A2-293[»]
    ProteinModelPortaliO87170.
    SMRiO87170. Positions 1-293.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiO87170.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni31 – 311Substrate binding

    Sequence similaritiesi

    Belongs to the PDC hydrolase family.Curated

    Family and domain databases

    InterProiIPR006992. Amidohydro_2.
    [Graphical view]
    PfamiPF04909. Amidohydro_2. 1 hit.
    [Graphical view]

    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
    EntryMethodResolution (Å)ChainPositionsPDBsum
    4D8LX-ray2.00A2-293[»]
    4DI8X-ray1.81A/B2-293[»]
    4DI9X-ray1.35A2-293[»]
    4DIAX-ray2.00A2-293[»]
    ProteinModelPortaliO87170.
    SMRiO87170. Positions 1-293.
    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

    InterProiIPR006992. Amidohydro_2.
    [Graphical view]
    PfamiPF04909. Amidohydro_2. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Publicationsi

    1. "Molecular cloning of the protocatechuate 4,5-dioxygenase genes of Pseudomonas paucimobilis."
      Noda Y., Nishikawa S., Shiozuka K., Kadokura H., Nakajima H., Yoda K., Katayama Y., Morohoshi N., Haraguchi T., Yamasaki M.
      J. Bacteriol. 172:2704-2709(1990) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    2. "Genetic and biochemical characterization of a 2-pyrone-4, 6-dicarboxylic acid hydrolase involved in the protocatechuate 4, 5-cleavage pathway of Sphingomonas paucimobilis SYK-6."
      Masai E., Shinohara S., Hara H., Nishikawa S., Katayama Y., Fukuda M.
      J. Bacteriol. 181:55-62(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, CATALYTIC ACTIVITY, DISRUPTION PHENOTYPE, BIOPHYSICOCHEMICAL PROPERTIES, ENZYME REGULATION, SUBUNIT.
      Strain: SYK-6.
    3. "Genetic and biochemical characterization of 4-carboxy-2-hydroxymuconate-6-semialdehyde dehydrogenase and its role in the protocatechuate 4,5-cleavage pathway in Sphingomonas paucimobilis SYK-6."
      Masai E., Momose K., Hara H., Nishikawa S., Katayama Y., Fukuda M.
      J. Bacteriol. 182:6651-6658(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    4. "The 4-oxalomesaconate hydratase gene, involved in the protocatechuate 4,5-cleavage pathway, is essential to vanillate and syringate degradation in Sphingomonas paucimobilis SYK-6."
      Hara H., Masai E., Katayama Y., Fukuda M.
      J. Bacteriol. 182:6950-6957(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    5. "Characterization of the 4-carboxy-4-hydroxy-2-oxoadipate aldolase gene and operon structure of the protocatechuate 4,5-cleavage pathway genes in Sphingomonas paucimobilis SYK-6."
      Hara H., Masai E., Miyauchi K., Katayama Y., Fukuda M.
      J. Bacteriol. 185:41-50(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    6. "2-pyrone-4,6-dicarboxylic acid, a catabolite of gallic acids in Pseudomonas species."
      Kersten P.J., Dagley S., Whittaker J.W., Arciero D.M., Lipscomb J.D.
      J. Bacteriol. 152:1154-1162(1982) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY, ENZYME REGULATION, BIOPHYSICOCHEMICAL PROPERTIES, INDUCTION.
    7. "Structure and catalytic mechanism of LigI: insight into the amidohydrolase enzymes of cog3618 and lignin degradation."
      Hobbs M.E., Malashkevich V., Williams H.J., Xu C., Sauder J.M., Burley S.K., Almo S.C., Raushel F.M.
      Biochemistry 51:3497-3507(2012) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.35 ANGSTROMS) OF 2-293 OF MUTANTS IN COMPLEX WITH SUBSTRATE, FUNCTION, CATALYTIC ACTIVITY, MUTAGENESIS OF ASP-246, ACTIVE SITE, BIOPHYSICOCHEMICAL PROPERTIES, ENZYME REGULATION, SUBUNIT.

    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: April 1, 2015
    This is version 62 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

    External Data

    Dasty 3

    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 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.