ID   LIGI_SPHSK              Reviewed;         293 AA.
AC   O87170; G2IQR0;
DT   26-JUN-2013, integrated into UniProtKB/Swiss-Prot.
DT   01-NOV-1998, sequence version 1.
DT   24-JAN-2024, entry version 92.
DE   RecName: Full=2-pyrone-4,6-dicarboxylate hydrolase {ECO:0000303|PubMed:9864312};
DE            Short=PDC hydrolase {ECO:0000303|PubMed:9864312};
DE            EC=3.1.1.57 {ECO:0000269|PubMed:22475079, ECO:0000269|PubMed:29658701};
DE   AltName: Full=2-pyrone-4,6-dicarboxylate lactonase {ECO:0000303|PubMed:22475079};
GN   Name=ligI {ECO:0000312|EMBL:BAK65932.1};
GN   ORFNames=SLG_12570 {ECO:0000312|EMBL:BAK65932.1};
OS   Sphingobium sp. (strain NBRC 103272 / SYK-6).
OC   Bacteria; Pseudomonadota; Alphaproteobacteria; Sphingomonadales;
OC   Sphingomonadaceae; Sphingobium.
OX   NCBI_TaxID=627192;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, CATALYTIC ACTIVITY, DISRUPTION
RP   PHENOTYPE, BIOPHYSICOCHEMICAL PROPERTIES, ACTIVITY REGULATION, SUBUNIT, AND
RP   PATHWAY.
RC   STRAIN=NBRC 103272 / SYK-6;
RX   PubMed=9864312; DOI=10.1128/jb.181.1.55-62.1999;
RA   Masai E., Shinohara S., Hara H., Nishikawa S., Katayama Y., Fukuda M.;
RT   "Genetic and biochemical characterization of a 2-pyrone-4, 6-dicarboxylic
RT   acid hydrolase involved in the protocatechuate 4, 5-cleavage pathway of
RT   Sphingomonas paucimobilis SYK-6.";
RL   J. Bacteriol. 181:55-62(1999).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC   STRAIN=NBRC 103272 / SYK-6;
RX   PubMed=12486039; DOI=10.1128/jb.185.1.41-50.2003;
RA   Hara H., Masai E., Miyauchi K., Katayama Y., Fukuda M.;
RT   "Characterization of the 4-carboxy-4-hydroxy-2-oxoadipate aldolase gene and
RT   operon structure of the protocatechuate 4,5-cleavage pathway genes in
RT   Sphingomonas paucimobilis SYK-6.";
RL   J. Bacteriol. 185:41-50(2003).
RN   [3]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=NBRC 103272 / SYK-6;
RX   PubMed=22207743; DOI=10.1128/jb.06254-11;
RA   Masai E., Kamimura N., Kasai D., Oguchi A., Ankai A., Fukui S.,
RA   Takahashi M., Yashiro I., Sasaki H., Harada T., Nakamura S., Katano Y.,
RA   Narita-Yamada S., Nakazawa H., Hara H., Katayama Y., Fukuda M.,
RA   Yamazaki S., Fujita N.;
RT   "Complete genome sequence of Sphingobium sp. strain SYK-6, a degrader of
RT   lignin-derived biaryls and monoaryls.";
RL   J. Bacteriol. 194:534-535(2012).
RN   [4]
RP   FUNCTION, AND CATALYTIC ACTIVITY.
RC   STRAIN=NBRC 103272 / SYK-6;
RX   PubMed=29658701; DOI=10.1021/acs.biochem.8b00295;
RA   Hogancamp T.N., Raushel F.M.;
RT   "Functional annotation of LigU as a 1,3-allylic isomerase during the
RT   degradation of lignin in the protocatechuate 4,5-cleavage pathway from the
RT   soil bacterium Sphingobium sp. SYK-6.";
RL   Biochemistry 57:2837-2845(2018).
RN   [5]
RP   X-RAY CRYSTALLOGRAPHY (1.35 ANGSTROMS) OF 2-293 OF WILD-TYPE AND MUTANTS
RP   ALA-246 AND ASN-246 IN COMPLEX WITH SUBSTRATE, FUNCTION, CATALYTIC
RP   ACTIVITY, MUTAGENESIS OF ASP-246, ACTIVE SITE, BIOPHYSICOCHEMICAL
RP   PROPERTIES, ACTIVITY REGULATION, AND REACTION MECHANISM.
RX   PubMed=22475079; DOI=10.1021/bi300307b;
RA   Hobbs M.E., Malashkevich V., Williams H.J., Xu C., Sauder J.M.,
RA   Burley S.K., Almo S.C., Raushel F.M.;
RT   "Structure and catalytic mechanism of LigI: insight into the amidohydrolase
RT   enzymes of cog3618 and lignin degradation.";
RL   Biochemistry 51:3497-3507(2012).
CC   -!- FUNCTION: Contributes to the degradation of lignin at the level of the
CC       protocatechuate 4,5-cleavage pathway (PubMed:9864312). Catalyzes the
CC       hydrolysis of 2-pyrone-4,6-dicarboxylate (PDC) to (4E)-oxalomesaconate
CC       (OMA) (PubMed:29658701, PubMed:22475079). The keto form of OMA can
CC       tautomerize into the enol form, 4-carboxy-2-hydroxymuconate (CHM),
CC       under certain pH conditions (PubMed:22475079). Also catalyzes the
CC       reverse reaction (PubMed:22475079, PubMed:9864312). Is essential for
CC       the growth of Sphingobium sp. SYK-6 on vanillate but is not responsible
CC       for the growth of this strain on syringate (PubMed:9864312).
CC       {ECO:0000269|PubMed:22475079, ECO:0000269|PubMed:29658701,
CC       ECO:0000269|PubMed:9864312}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=2-oxo-2H-pyran-4,6-dicarboxylate + H2O = (1E)-4-oxobut-1-ene-
CC         1,2,4-tricarboxylate + H(+); Xref=Rhea:RHEA:10644, ChEBI:CHEBI:15377,
CC         ChEBI:CHEBI:15378, ChEBI:CHEBI:57471, ChEBI:CHEBI:58304; EC=3.1.1.57;
CC         Evidence={ECO:0000269|PubMed:22475079, ECO:0000269|PubMed:29658701};
CC   -!- ACTIVITY REGULATION: Strongly inhibited by 1 mM Zn(2+) ions
CC       (PubMed:9864312). Also inhibited by pyridine-2,4-dicarboxylic acid, 5-
CC       hydroxyisophthalic acid and 5,5'-dithiobis(2-nitrobenzoic acid) (Ellman
CC       reagent) (PubMed:22475079, PubMed:9864312).
CC       {ECO:0000269|PubMed:22475079, ECO:0000269|PubMed:9864312}.
CC   -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC       Kinetic parameters:
CC         KM=18 uM for a mixture of
CC         (4E)-oxalomesaconate/4-carboxy-2-hydroxymuconate (at pH 8.25)
CC         {ECO:0000269|PubMed:22475079};
CC         KM=48 uM for 2-pyrone-4,6-dicarboxylate (at pH 8.25)
CC         {ECO:0000269|PubMed:22475079};
CC         KM=49 uM for 4-carboxy-2-hydroxymuconate (at pH 7 and at 30 degrees
CC         Celsius) {ECO:0000269|PubMed:9864312};
CC         KM=74 uM for 2-pyrone-4,6-dicarboxylate (at pH 8.5 and at 30 degrees
CC         Celsius) {ECO:0000269|PubMed:9864312};
CC         Note=kcat is 342 sec(-1) for the hydrolysis of
CC         2-pyrone-4,6-dicarboxylate (at pH 8.25). kcat is 116 sec(-1) for the
CC         synthesis of 2-pyrone-4,6-dicarboxylat from OMA/CHM (at pH 8.25).
CC         {ECO:0000269|PubMed:22475079};
CC       pH dependence:
CC         Optimum pH for hydrolysis of PDC is 8.5 and optimum pH for synthesis
CC         of PDC is between 6.0 to 7.5. {ECO:0000269|PubMed:9864312};
CC       Temperature dependence:
CC         Optimum temperature is 50 degrees Celsius.
CC         {ECO:0000269|PubMed:9864312};
CC   -!- PATHWAY: Secondary metabolite metabolism; lignin degradation.
CC       {ECO:0000269|PubMed:9864312}.
CC   -!- SUBUNIT: Monomer. {ECO:0000269|PubMed:9864312}.
CC   -!- DISRUPTION PHENOTYPE: Cells lacking this gene show a complete loss of
CC       PDC hydrolase activity and a growth defect on vanillic acid. Growth on
CC       syringic acid is not affected. {ECO:0000269|PubMed:9864312}.
CC   -!- MISCELLANEOUS: This is the first enzyme from the amidohydrolase
CC       superfamily that does not require a divalent metal ion for catalytic
CC       activity. {ECO:0000305|PubMed:22475079}.
CC   -!- SIMILARITY: Belongs to the metallo-dependent hydrolases superfamily.
CC       PDC hydrolase family. {ECO:0000305}.
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DR   EMBL; AB015964; BAA33799.1; -; Genomic_DNA.
DR   EMBL; AB073227; BAB88736.1; -; Genomic_DNA.
DR   EMBL; AP012222; BAK65932.1; -; Genomic_DNA.
DR   RefSeq; WP_014075583.1; NC_015976.1.
DR   PDB; 4D8L; X-ray; 2.00 A; A=2-293.
DR   PDB; 4DI8; X-ray; 1.81 A; A/B=2-293.
DR   PDB; 4DI9; X-ray; 1.35 A; A=2-293.
DR   PDB; 4DIA; X-ray; 2.00 A; A=2-293.
DR   PDBsum; 4D8L; -.
DR   PDBsum; 4DI8; -.
DR   PDBsum; 4DI9; -.
DR   PDBsum; 4DIA; -.
DR   AlphaFoldDB; O87170; -.
DR   SMR; O87170; -.
DR   STRING; 627192.SLG_12570; -.
DR   KEGG; ssy:SLG_12570; -.
DR   eggNOG; COG3618; Bacteria.
DR   HOGENOM; CLU_064039_2_1_5; -.
DR   OrthoDB; 9787654at2; -.
DR   BioCyc; MetaCyc:MONOMER-3467; -.
DR   BRENDA; 3.1.1.57; 7695.
DR   UniPathway; UPA00892; -.
DR   EvolutionaryTrace; O87170; -.
DR   Proteomes; UP000001275; Chromosome.
DR   GO; GO:0047554; F:2-pyrone-4,6-dicarboxylate lactonase activity; IDA:UniProtKB.
DR   GO; GO:0019619; P:3,4-dihydroxybenzoate catabolic process; IDA:UniProtKB.
DR   GO; GO:0046274; P:lignin catabolic process; IEA:UniProtKB-UniPathway.
DR   Gene3D; 3.20.20.140; Metal-dependent hydrolases; 1.
DR   InterPro; IPR006680; Amidohydro-rel.
DR   InterPro; IPR032466; Metal_Hydrolase.
DR   PANTHER; PTHR35563; BARREL METAL-DEPENDENT HYDROLASE, PUTATIVE (AFU_ORTHOLOGUE AFUA_1G16240)-RELATED; 1.
DR   PANTHER; PTHR35563:SF2; BARREL METAL-DEPENDENT HYDROLASE, PUTATIVE (AFU_ORTHOLOGUE AFUA_1G16240)-RELATED; 1.
DR   Pfam; PF04909; Amidohydro_2; 1.
DR   SUPFAM; SSF51556; Metallo-dependent hydrolases; 1.
PE   1: Evidence at protein level;
KW   3D-structure; Aromatic hydrocarbons catabolism; Hydrolase;
KW   Reference proteome.
FT   CHAIN           1..293
FT                   /note="2-pyrone-4,6-dicarboxylate hydrolase"
FT                   /id="PRO_0000422783"
FT   REGION          1..20
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        1..15
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   ACT_SITE        246
FT                   /note="Proton acceptor"
FT                   /evidence="ECO:0000305|PubMed:22475079"
FT   BINDING         29..31
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000269|PubMed:22475079"
FT   BINDING         47
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000269|PubMed:22475079"
FT   BINDING         75
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000269|PubMed:22475079"
FT   BINDING         122
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000269|PubMed:22475079"
FT   BINDING         128
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000269|PubMed:22475079"
FT   BINDING         154
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000269|PubMed:22475079"
FT   BINDING         178
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000269|PubMed:22475079"
FT   BINDING         251
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000269|PubMed:22475079"
FT   MUTAGEN         246
FT                   /note="D->A: Loss of catalytic activity."
FT                   /evidence="ECO:0000269|PubMed:22475079"
FT   MUTAGEN         246
FT                   /note="D->N: Almost inactive."
FT                   /evidence="ECO:0000269|PubMed:22475079"
FT   HELIX           3..5
FT                   /evidence="ECO:0007829|PDB:4DI9"
FT   STRAND          26..30
FT                   /evidence="ECO:0007829|PDB:4DI9"
FT   TURN            36..38
FT                   /evidence="ECO:0007829|PDB:4DI9"
FT   HELIX           54..64
FT                   /evidence="ECO:0007829|PDB:4DI9"
FT   STRAND          67..72
FT                   /evidence="ECO:0007829|PDB:4DI9"
FT   HELIX           75..77
FT                   /evidence="ECO:0007829|PDB:4DI9"
FT   HELIX           82..90
FT                   /evidence="ECO:0007829|PDB:4DI9"
FT   TURN            91..93
FT                   /evidence="ECO:0007829|PDB:4DI9"
FT   STRAND          94..99
FT                   /evidence="ECO:0007829|PDB:4DI9"
FT   HELIX           107..115
FT                   /evidence="ECO:0007829|PDB:4DI9"
FT   STRAND          118..124
FT                   /evidence="ECO:0007829|PDB:4DI9"
FT   TURN            127..129
FT                   /evidence="ECO:0007829|PDB:4DI9"
FT   HELIX           135..142
FT                   /evidence="ECO:0007829|PDB:4DI9"
FT   STRAND          150..154
FT                   /evidence="ECO:0007829|PDB:4DI9"
FT   HELIX           157..159
FT                   /evidence="ECO:0007829|PDB:4DI9"
FT   HELIX           160..169
FT                   /evidence="ECO:0007829|PDB:4DI9"
FT   STRAND          174..176
FT                   /evidence="ECO:0007829|PDB:4DI9"
FT   HELIX           177..180
FT                   /evidence="ECO:0007829|PDB:4DI9"
FT   HELIX           184..186
FT                   /evidence="ECO:0007829|PDB:4DI9"
FT   HELIX           191..202
FT                   /evidence="ECO:0007829|PDB:4DI9"
FT   STRAND          206..209
FT                   /evidence="ECO:0007829|PDB:4DI9"
FT   HELIX           213..216
FT                   /evidence="ECO:0007829|PDB:4DI9"
FT   HELIX           224..236
FT                   /evidence="ECO:0007829|PDB:4DI9"
FT   TURN            237..239
FT                   /evidence="ECO:0007829|PDB:4DI9"
FT   STRAND          240..242
FT                   /evidence="ECO:0007829|PDB:4DI9"
FT   HELIX           259..264
FT                   /evidence="ECO:0007829|PDB:4DI9"
FT   HELIX           266..269
FT                   /evidence="ECO:0007829|PDB:4DI9"
FT   HELIX           273..280
FT                   /evidence="ECO:0007829|PDB:4DI9"
FT   HELIX           282..288
FT                   /evidence="ECO:0007829|PDB:4DI9"
FT   HELIX           290..292
FT                   /evidence="ECO:0007829|PDB:4DI9"
SQ   SEQUENCE   293 AA;  32775 MW;  95DE7EB8449AADD5 CRC64;
     MTNDERILSW NETPSKPRYT PPPGAIDAHC HVFGPMAQFP FSPKAKYLPR DAGPDMLFAL
     RDHLGFARNV IVQASCHGTD NAATLDAIAR AQGKARGIAV VDPAIDEAEL AALHEGGMRG
     IRFNFLKRLV DDAPKDKFLE VAGRLPAGWH VVIYFEADIL EELRPFMDAI PVPIVIDHMG
     RPDVRQGPDG ADMKAFRRLL DSREDIWFKA TCPDRLDPAG PPWDDFARSV APLVADYADR
     VIWGTDWPHP NMQDAIPDDG LVVDMIPRIA PTPELQHKML VTNPMRLYWS EEM
//