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O87170 (PDCH_SPHPI) Reviewed, UniProtKB/Swiss-Prot

Last modified March 19, 2014. Version 59. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
2-pyrone-4,6-dicarbaxylate hydrolase
Alternative name(s):
2-pyrone-4,6-dicarboxylate lactonohydrolase
PDC hydrolase
EC=3.1.1.57
Gene names
Name:ligI
OrganismSphingomonas paucimobilis (Pseudomonas paucimobilis)
Taxonomic identifier13689 [NCBI]
Taxonomic lineageBacteriaProteobacteriaAlphaproteobacteriaSphingomonadalesSphingomonadaceaeSphingomonas

Protein attributes

Sequence length293 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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 (Ref.7). Ref.2 Ref.6 Ref.7

Catalytic activity

2-oxo-2H-pyran-4,6-dicarboxylate + H2O = (1E)-4-oxobut-1-ene-1,2,4-tricarboxylate. Ref.2 Ref.6 Ref.7

Enzyme regulation

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). Ref.2 Ref.6 Ref.7

Subunit structure

Homodimer. Ref.2 Ref.7

Induction

Induced by 4-hydroxybenzoic acid. Ref.2 Ref.6 Ref.7

Disruption phenotype

Cells lacking this gene show a complete loss of PDC hydrolase activity and a growth defect on vanillic acid. Ref.2

Miscellaneous

This is the first enzyme from the amidohydrolase superfamily that does not require a divalent metal ion for catalytic activity (Ref.7).

Sequence similarities

Belongs to the PDC hydrolase family.

Biophysicochemical properties

Kinetic parameters:

Kcat is 342 sec(-1) and 116 sec(-1) with PDC and OMA/CHM, respectively (at pH 8.25)(Ref.7).

KM=18 µM for OMA/CHM (at pH 8.25)(Ref.7) Ref.2 Ref.6 Ref.7

KM=48 µM for PDC (at pH 8.25)(Ref.7)

KM=49 µM for CHM (at pH 7 and at 30 degrees Celsius)(Ref.2)

KM=74 µM for PDC (at pH 8.5 and at 30 degrees Celsius)(Ref.2)

KM=90 µM for PDC (Ref.6)

pH dependence:

Optimum pH for hydrolysis of PDC is 8.5 and optimum pH for synthesis of PDC is between 6.0 to 7.5.

Temperature dependence:

Optimum temperature is 50 degrees Celsius.

Ontologies

Keywords
   Molecular functionHydrolase
   Technical term3D-structure
Gene Ontology (GO)
   Biological_processprotocatechuate catabolic process

Inferred from direct assay Ref.2. Source: UniProtKB

   Molecular_function2-pyrone-4,6-dicarboxylate lactonase activity

Inferred from direct assay Ref.7. Source: UniProtKB

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 2932932-pyrone-4,6-dicarbaxylate hydrolase
PRO_0000422783

Regions

Region311Substrate binding

Sites

Active site2461 Ref.7
Binding site471Substrate
Binding site751Substrate
Binding site1221Substrate
Binding site1281Substrate
Binding site1541Substrate
Binding site1781Substrate
Binding site2511Substrate

Experimental info

Mutagenesis2461D → A: Almost inactive. Ref.7
Mutagenesis2461D → N: Almost inactive. Ref.7

Secondary structure

....................................................... 293
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
O87170 [UniParc].

Last modified November 1, 1998. Version 1.
Checksum: 95DE7EB8449AADD5

FASTA29332,775
        10         20         30         40         50         60 
MTNDERILSW NETPSKPRYT PPPGAIDAHC HVFGPMAQFP FSPKAKYLPR DAGPDMLFAL 

        70         80         90        100        110        120 
RDHLGFARNV IVQASCHGTD NAATLDAIAR AQGKARGIAV VDPAIDEAEL AALHEGGMRG 

       130        140        150        160        170        180 
IRFNFLKRLV DDAPKDKFLE VAGRLPAGWH VVIYFEADIL EELRPFMDAI PVPIVIDHMG 

       190        200        210        220        230        240 
RPDVRQGPDG ADMKAFRRLL DSREDIWFKA TCPDRLDPAG PPWDDFARSV APLVADYADR 

       250        260        270        280        290 
VIWGTDWPHP NMQDAIPDDG LVVDMIPRIA PTPELQHKML VTNPMRLYWS EEM 

« Hide

References

[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.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AB015964 Genomic DNA. Translation: BAA33799.1.
AB073227 Genomic DNA. Translation: BAB88736.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
4D8LX-ray2.00A2-293[»]
4DI8X-ray1.81A/B2-293[»]
4DI9X-ray1.35A2-293[»]
4DIAX-ray2.00A2-293[»]
ProteinModelPortalO87170.
SMRO87170. Positions 1-293.
ModBaseSearch...
MobiDBSearch...

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Enzyme and pathway databases

BioCycMetaCyc:MONOMER-3467.

Family and domain databases

InterProIPR006992. Amidohydro_2.
[Graphical view]
PfamPF04909. Amidohydro_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceO87170.

Entry information

Entry namePDCH_SPHPI
AccessionPrimary (citable) accession number: O87170
Entry history
Integrated into UniProtKB/Swiss-Prot: June 26, 2013
Last sequence update: November 1, 1998
Last modified: March 19, 2014
This is version 59 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references