LIGJ_SPHSK
ID LIGJ_SPHSK Reviewed; 341 AA.
AC G2IQQ5; Q9KWL6;
DT 13-FEB-2019, integrated into UniProtKB/Swiss-Prot.
DT 16-NOV-2011, sequence version 1.
DT 03-AUG-2022, entry version 49.
DE RecName: Full=2-keto-4-carboxy-3-hexenedioate hydratase {ECO:0000305|PubMed:29658701};
DE Short=KCH hydratase {ECO:0000303|PubMed:30207699};
DE EC=4.2.1.- {ECO:0000269|PubMed:29658701, ECO:0000269|PubMed:30207699};
GN Name=ligJ {ECO:0000303|PubMed:29658701};
GN ORFNames=SLG_12520 {ECO:0000312|EMBL:BAK65927.1};
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], DISRUPTION PHENOTYPE, AND PATHWAY.
RC STRAIN=NBRC 103272 / SYK-6;
RX PubMed=11092855; DOI=10.1128/jb.182.24.6950-6957.2000;
RA Hara H., Masai E., Katayama Y., Fukuda M.;
RT "The 4-oxalomesaconate hydratase gene, involved in the protocatechuate 4,5-
RT cleavage pathway, is essential to vanillate and syringate degradation in
RT Sphingomonas paucimobilis SYK-6.";
RL J. Bacteriol. 182:6950-6957(2000).
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, CATALYTIC ACTIVITY, AND PATHWAY.
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] {ECO:0007744|PDB:6DWV, ECO:0007744|PDB:6DXQ, ECO:0007744|PDB:6DXS}
RP X-RAY CRYSTALLOGRAPHY (1.65 ANGSTROMS) OF WILD-TYPE AND MUTANT GLN-284 IN
RP COMPLEXES WITH ZINC; (3Z)-2-KETO-4-CARBOXY-3-HEXENEDIOATE (KCH) AND
RP (4S)-4-CARBOXY-4-HYDROXY-2-OXOADIPATE (CHA), MUTAGENESIS OF THR-190;
RP TYR-194; HIS-223 AND GLU-284, FUNCTION, CATALYTIC ACTIVITY, COFACTOR,
RP BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT, AND REACTION MECHANISM.
RC STRAIN=NBRC 103272 / SYK-6;
RX PubMed=30207699; DOI=10.1021/acs.biochem.8b00713;
RA Hogancamp T.N., Mabanglo M.F., Raushel F.M.;
RT "Structure and reaction mechanism of the LigJ hydratase: an enzyme critical
RT for the bacterial degradation of lignin in the protocatechuate 4,5-cleavage
RT pathway.";
RL Biochemistry 57:5841-5850(2018).
CC -!- FUNCTION: Contributes to the degradation of lignin at the level of the
CC protocatechuate 4,5-cleavage pathway. Catalyzes the hydration of the
CC double bond of (3Z)-2-keto-4-carboxy-3-hexenedioate (KCH) to (4S)-4-
CC carboxy-4-hydroxy-2-oxoadipate (CHA, also named (2S)-2-hydroxy-4-
CC oxobutane-1,2,4-tricarboxylate) (PubMed:29658701, PubMed:30207699). Is
CC involved in the catabolism of both vanillate and syringate
CC (PubMed:11092855). {ECO:0000269|PubMed:11092855,
CC ECO:0000269|PubMed:29658701, ECO:0000269|PubMed:30207699}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(3Z)-2-oxo-4-carboxy-3-hexenedioate + H2O = (2S)-2-hydroxy-4-
CC oxobutane-1,2,4-tricarboxylate; Xref=Rhea:RHEA:58508,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:142690, ChEBI:CHEBI:142706;
CC Evidence={ECO:0000269|PubMed:29658701, ECO:0000269|PubMed:30207699};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000269|PubMed:30207699};
CC Note=Binds 1 zinc ion per subunit. The metal center contained within
CC the active site of LigJ is not used to activate the water molecule but
CC is utilized to activate the substrate via polarization of the carbonyl
CC oxygen. {ECO:0000269|PubMed:30207699};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=9.8 uM for (3Z)-2-keto-4-carboxy-3-hexenedioate (at pH 8.0)
CC {ECO:0000269|PubMed:30207699};
CC Note=kcat is 25.6 sec(-1) (at pH 8.0). {ECO:0000269|PubMed:30207699};
CC -!- PATHWAY: Secondary metabolite metabolism; lignin degradation.
CC {ECO:0000269|PubMed:11092855, ECO:0000305|PubMed:29658701}.
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:30207699}.
CC -!- DISRUPTION PHENOTYPE: Cells lacking this gene catabolize vanillate and
CC syringate with an accumulation of the enol form of oxalomesaconate
CC (OMA), 2-pyrone-4,6-dicarboxylate (PDC), and a product that is likely
CC to be KCH. {ECO:0000269|PubMed:11092855}.
CC -!- SIMILARITY: Belongs to the metallo-dependent hydrolases superfamily.
CC {ECO:0000305}.
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DR EMBL; AB035121; BAA97116.1; -; Genomic_DNA.
DR EMBL; AB073227; BAB88741.1; -; Genomic_DNA.
DR EMBL; AP012222; BAK65927.1; -; Genomic_DNA.
DR RefSeq; WP_014075578.1; NC_015976.1.
DR PDB; 6DWV; X-ray; 2.20 A; A/B/C/D=1-341.
DR PDB; 6DXQ; X-ray; 2.02 A; A/B/C/D=2-341.
DR PDB; 6DXS; X-ray; 1.65 A; A/B/C/D=2-341.
DR PDBsum; 6DWV; -.
DR PDBsum; 6DXQ; -.
DR PDBsum; 6DXS; -.
DR AlphaFoldDB; G2IQQ5; -.
DR SMR; G2IQQ5; -.
DR STRING; 627192.SLG_12520; -.
DR EnsemblBacteria; BAK65927; BAK65927; SLG_12520.
DR KEGG; ssy:SLG_12520; -.
DR eggNOG; COG2159; Bacteria.
DR HOGENOM; CLU_813586_0_0_5; -.
DR OrthoDB; 1832218at2; -.
DR BRENDA; 4.2.1.83; 2280.
DR UniPathway; UPA00892; -.
DR Proteomes; UP000001275; Chromosome.
DR GO; GO:0016831; F:carboxy-lyase activity; IEA:InterPro.
DR GO; GO:0016787; F:hydrolase activity; IEA:InterPro.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0046274; P:lignin catabolic process; IEA:UniProtKB-UniPathway.
DR InterPro; IPR032465; ACMSD.
DR InterPro; IPR006680; Amidohydro-rel.
DR InterPro; IPR032466; Metal_Hydrolase.
DR PANTHER; PTHR21240; PTHR21240; 1.
DR Pfam; PF04909; Amidohydro_2; 1.
DR SUPFAM; SSF51556; SSF51556; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Aromatic hydrocarbons catabolism; Lyase; Metal-binding;
KW Reference proteome; Zinc.
FT CHAIN 1..341
FT /note="2-keto-4-carboxy-3-hexenedioate hydratase"
FT /id="PRO_0000446301"
FT ACT_SITE 284
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000305|PubMed:30207699"
FT BINDING 8
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000269|PubMed:30207699,
FT ECO:0000312|PDB:6DWV"
FT BINDING 10
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000269|PubMed:30207699,
FT ECO:0000312|PDB:6DWV"
FT BINDING 71..73
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:30207699,
FT ECO:0000312|PDB:6DXS"
FT BINDING 178
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000269|PubMed:30207699,
FT ECO:0000312|PDB:6DWV"
FT BINDING 194
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:30207699,
FT ECO:0000312|PDB:6DXS"
FT BINDING 223
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:30207699,
FT ECO:0000312|PDB:6DXS"
FT BINDING 290
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:30207699,
FT ECO:0000312|PDB:6DXS"
FT MUTAGEN 190
FT /note="T->A: 2.4-fold reduction in catalytic rate."
FT /evidence="ECO:0000269|PubMed:30207699"
FT MUTAGEN 194
FT /note="Y->F: 7.8-fold reduction in catalytic rate."
FT /evidence="ECO:0000269|PubMed:30207699"
FT MUTAGEN 223
FT /note="H->N: 91-fold reduction in catalytic rate. 30-fold
FT decrease in affinity for the substrate KCH."
FT /evidence="ECO:0000269|PubMed:30207699"
FT MUTAGEN 284
FT /note="E->Q: Loss of enzymatic activity."
FT /evidence="ECO:0000269|PubMed:30207699"
FT STRAND 5..11
FT /evidence="ECO:0007829|PDB:6DXQ"
FT HELIX 16..30
FT /evidence="ECO:0007829|PDB:6DXS"
FT HELIX 43..52
FT /evidence="ECO:0007829|PDB:6DXS"
FT HELIX 54..61
FT /evidence="ECO:0007829|PDB:6DXS"
FT STRAND 65..70
FT /evidence="ECO:0007829|PDB:6DXS"
FT HELIX 72..75
FT /evidence="ECO:0007829|PDB:6DXS"
FT HELIX 82..102
FT /evidence="ECO:0007829|PDB:6DXS"
FT TURN 104..106
FT /evidence="ECO:0007829|PDB:6DXS"
FT STRAND 107..112
FT /evidence="ECO:0007829|PDB:6DXS"
FT HELIX 122..133
FT /evidence="ECO:0007829|PDB:6DXS"
FT STRAND 139..142
FT /evidence="ECO:0007829|PDB:6DXS"
FT STRAND 148..150
FT /evidence="ECO:0007829|PDB:6DXS"
FT HELIX 159..161
FT /evidence="ECO:0007829|PDB:6DXS"
FT HELIX 162..171
FT /evidence="ECO:0007829|PDB:6DXS"
FT STRAND 175..177
FT /evidence="ECO:0007829|PDB:6DXS"
FT TURN 189..192
FT /evidence="ECO:0007829|PDB:6DXS"
FT HELIX 193..206
FT /evidence="ECO:0007829|PDB:6DXS"
FT TURN 211..213
FT /evidence="ECO:0007829|PDB:6DXS"
FT STRAND 219..221
FT /evidence="ECO:0007829|PDB:6DXS"
FT HELIX 222..225
FT /evidence="ECO:0007829|PDB:6DXS"
FT TURN 226..231
FT /evidence="ECO:0007829|PDB:6DXS"
FT HELIX 232..241
FT /evidence="ECO:0007829|PDB:6DXS"
FT HELIX 247..250
FT /evidence="ECO:0007829|PDB:6DXS"
FT TURN 251..254
FT /evidence="ECO:0007829|PDB:6DXS"
FT STRAND 255..258
FT /evidence="ECO:0007829|PDB:6DXS"
FT HELIX 264..273
FT /evidence="ECO:0007829|PDB:6DXS"
FT HELIX 276..278
FT /evidence="ECO:0007829|PDB:6DXS"
FT TURN 285..287
FT /evidence="ECO:0007829|PDB:6DXQ"
FT TURN 294..296
FT /evidence="ECO:0007829|PDB:6DXS"
FT STRAND 297..299
FT /evidence="ECO:0007829|PDB:6DXS"
FT HELIX 303..309
FT /evidence="ECO:0007829|PDB:6DXS"
FT HELIX 314..321
FT /evidence="ECO:0007829|PDB:6DXS"
FT HELIX 323..328
FT /evidence="ECO:0007829|PDB:6DXS"
FT HELIX 330..337
FT /evidence="ECO:0007829|PDB:6DXS"
FT TURN 338..340
FT /evidence="ECO:0007829|PDB:6DXS"
SQ SEQUENCE 341 AA; 38052 MW; 796ECA9AA65FB5DA CRC64;
MMMIIDCHGH YTVLPKAHDE WREQQKAAFK AGQPAPPYPE ISDDEIRETI EANQLRLIKE
RGADMTIFSP RASAMAPHVG DQSVAVPWAQ ACNNLIARVV DLFPETFAGV CMLPQSPEAD
MTSSIAELER CVNELGFIGC NLNPDPGGGH FKHPPLTDRF WYPFYEKMVE LDVPAMIHVS
GSCNPAMHAT GAYYLAADTI AFMQLLQGNL FADFPTLRFI IPHGGGAVPY HWGRFRGLAD
MLKQPSLDTL LMNNVFFDTC VYHQPGINLL ADVIDNKNIL FGSEMVGAVR GIDPTTGHYF
DDTKRYIDAL DISDQERHAI FEGNTRRVFP RLDAKLKARG L
