LIGI_SPHSK
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 03-AUG-2022, entry version 87.
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; Proteobacteria; 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 (4E)-oxalomesaconate/4-carboxy-2-
CC hydroxymuconate (at pH 8.25) {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 2-pyrone-4,6-
CC dicarboxylate (at pH 8.25). kcat is 116 sec(-1) for the synthesis of
CC 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 EnsemblBacteria; BAK65932; BAK65932; SLG_12570.
DR KEGG; ssy:SLG_12570; -.
DR eggNOG; COG3618; Bacteria.
DR HOGENOM; CLU_064039_2_1_5; -.
DR OrthoDB; 1979322at2; -.
DR BioCyc; MetaCyc:MON-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 InterPro; IPR006680; Amidohydro-rel.
DR InterPro; IPR032466; Metal_Hydrolase.
DR Pfam; PF04909; Amidohydro_2; 1.
DR SUPFAM; SSF51556; SSF51556; 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
