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O87170

- PDCH_SPHPI

UniProt

O87170 - PDCH_SPHPI

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Protein

2-pyrone-4,6-dicarbaxylate hydrolase

Gene

ligI

Organism
Sphingomonas paucimobilis (Pseudomonas paucimobilis)
Status
Reviewed - 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

  1. 2-pyrone-4,6-dicarboxylate lactonase activity Source: UniProtKB

GO - Biological processi

  1. protocatechuate catabolic process Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Enzyme and pathway databases

BioCyciMetaCyc:MONOMER-3467.

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
Entry Method Resolution (Å) Chain Positions PDBsum
4D8L X-ray 2.00 A 2-293 [» ]
4DI8 X-ray 1.81 A/B 2-293 [» ]
4DI9 X-ray 1.35 A 2-293 [» ]
4DIA X-ray 2.00 A 2-293 [» ]
ProteinModelPortali O87170.
SMRi O87170. Positions 1-293.
ModBasei Search...
MobiDBi Search...

Protocols and materials databases

Structural Biology Knowledgebase Search...

Enzyme and pathway databases

BioCyci MetaCyc:MONOMER-3467.

Miscellaneous databases

EvolutionaryTracei O87170.

Family and domain databases

InterProi IPR006992. Amidohydro_2.
[Graphical view ]
Pfami PF04909. Amidohydro_2. 1 hit.
[Graphical view ]
ProtoNeti Search...

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: November 26, 2014
This is version 61 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