LIGM_SPHSK
ID LIGM_SPHSK Reviewed; 471 AA.
AC G2IQS7; Q60FX1;
DT 08-MAY-2019, integrated into UniProtKB/Swiss-Prot.
DT 16-NOV-2011, sequence version 1.
DT 03-AUG-2022, entry version 55.
DE RecName: Full=Vanillate/3-O-methylgallate O-demethylase {ECO:0000303|PubMed:15743951};
DE Short=Vanillate/3MGA O-demethylase {ECO:0000303|PubMed:15743951};
DE EC=2.1.1.341 {ECO:0000269|PubMed:15743951, ECO:0000269|PubMed:28373573, ECO:0000269|PubMed:28429420};
GN Name=ligM {ECO:0000303|PubMed:15743951};
GN ORFNames=SLG_12740 {ECO:0000312|EMBL:BAK65949.1};
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, PATHWAY,
RP AND DISRUPTION PHENOTYPE.
RC STRAIN=NBRC 103272 / SYK-6;
RX PubMed=15743951; DOI=10.1128/jb.187.6.2030-2037.2005;
RA Abe T., Masai E., Miyauchi K., Katayama Y., Fukuda M.;
RT "A tetrahydrofolate-dependent O-demethylase, LigM, is crucial for
RT catabolism of vanillate and syringate in Sphingomonas paucimobilis SYK-6.";
RL J. Bacteriol. 187:2030-2037(2005).
RN [2]
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 [3] {ECO:0007744|PDB:5TL4}
RP X-RAY CRYSTALLOGRAPHY (1.75 ANGSTROMS), FUNCTION, CATALYTIC ACTIVITY,
RP BIOPHYSICOCHEMICAL PROPERTIES, AND MUTAGENESIS OF TYR-29; TYR-31; HIS-60;
RP MET-61; VAL-62; ARG-122; ARG-147 AND TYR-247.
RX PubMed=28373573; DOI=10.1073/pnas.1619263114;
RA Kohler A.C., Mills M.J.L., Adams P.D., Simmons B.A., Sale K.L.;
RT "Structure of aryl O-demethylase offers molecular insight into a catalytic
RT tyrosine-dependent mechanism.";
RL Proc. Natl. Acad. Sci. U.S.A. 114:E3205-E3214(2017).
RN [4] {ECO:0000312|PDB:5X1L, ECO:0000312|PDB:5X1M, ECO:0000312|PDB:5X1N, ECO:0007744|PDB:5X1I, ECO:0007744|PDB:5X1J, ECO:0007744|PDB:5X1K}
RP X-RAY CRYSTALLOGRAPHY (1.90 ANGSTROMS) OF APOENZYME AND IN COMPLEXES WITH
RP VANILLATE; 3MGA; PCA AND TETRAHYDROFOLATE, CATALYTIC ACTIVITY, SUBUNIT, AND
RP MUTAGENESIS OF TYR-31; HIS-60 AND TYR-247.
RC STRAIN=NBRC 103272 / SYK-6;
RX PubMed=28429420; DOI=10.1111/febs.14085;
RA Harada A., Kamimura N., Takeuchi K., Yu H.Y., Masai E., Senda T.;
RT "The crystal structure of a new O-demethylase from Sphingobium sp. strain
RT SYK-6.";
RL FEBS J. 284:1855-1867(2017).
CC -!- FUNCTION: Involved in the catabolism of vanillate and syringate.
CC Catalyzes the transfer of a methyl moiety from vanillate or 3-O-
CC methylgallate (3MGA) to tetrahydrofolate, forming protocatechuate (PCA)
CC or gallate, respectively, and methyl-tetrahydrofolate. Has similar
CC activities with both substrates (PubMed:15743951). Cannot use syringate
CC (PubMed:15743951). Uses an ordered, sequential kinetic mechanism
CC (PubMed:28373573). {ECO:0000269|PubMed:15743951,
CC ECO:0000269|PubMed:28373573}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(6S)-5,6,7,8-tetrahydrofolate + vanillate = (6S)-5-methyl-
CC 5,6,7,8-tetrahydrofolate + 3,4-dihydroxybenzoate;
CC Xref=Rhea:RHEA:52276, ChEBI:CHEBI:16632, ChEBI:CHEBI:18608,
CC ChEBI:CHEBI:36241, ChEBI:CHEBI:57453; EC=2.1.1.341;
CC Evidence={ECO:0000269|PubMed:15743951, ECO:0000269|PubMed:28373573,
CC ECO:0000269|PubMed:28429420};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:52277;
CC Evidence={ECO:0000269|PubMed:15743951, ECO:0000269|PubMed:28373573,
CC ECO:0000269|PubMed:28429420};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(6S)-5,6,7,8-tetrahydrofolate + 3-O-methylgallate = (6S)-5-
CC methyl-5,6,7,8-tetrahydrofolate + 3,4,5-trihydroxybenzoate;
CC Xref=Rhea:RHEA:52280, ChEBI:CHEBI:16918, ChEBI:CHEBI:18608,
CC ChEBI:CHEBI:19950, ChEBI:CHEBI:57453; EC=2.1.1.341;
CC Evidence={ECO:0000269|PubMed:15743951};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:52281;
CC Evidence={ECO:0000269|PubMed:15743951};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.63 mM for vanillate {ECO:0000269|PubMed:28373573};
CC KM=0.72 mM for tetrahydrofolate {ECO:0000269|PubMed:28373573};
CC Note=kcat is 5.76 sec(-1) with vanillate as substrate.
CC {ECO:0000269|PubMed:28373573};
CC pH dependence:
CC Optimum pH is 8 with vanillate as substrate.
CC {ECO:0000269|PubMed:28373573};
CC Temperature dependence:
CC Optimum temperature is 30 degrees Celsius with vanillate as
CC substrate. {ECO:0000269|PubMed:28373573};
CC -!- PATHWAY: Secondary metabolite metabolism; lignin degradation.
CC {ECO:0000305|PubMed:15743951}.
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:28429420}.
CC -!- DISRUPTION PHENOTYPE: Disruption of the gene leads to significant
CC growth retardation on both vanillate and syringate.
CC {ECO:0000269|PubMed:15743951}.
CC -!- SIMILARITY: Belongs to the GcvT family. {ECO:0000305}.
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DR EMBL; AB186750; BAD61059.1; -; Genomic_DNA.
DR EMBL; AP012222; BAK65949.1; -; Genomic_DNA.
DR RefSeq; WP_014075600.1; NC_015976.1.
DR PDB; 5TL4; X-ray; 1.75 A; A/B/C/D=1-471.
DR PDB; 5X1I; X-ray; 1.90 A; A/B/C=1-471.
DR PDB; 5X1J; X-ray; 1.90 A; A/B/C=1-471.
DR PDB; 5X1K; X-ray; 2.15 A; A/B/C=1-471.
DR PDB; 5X1L; X-ray; 1.90 A; A/B/C=1-471.
DR PDB; 5X1M; X-ray; 1.90 A; A/B/C=1-471.
DR PDB; 5X1N; X-ray; 2.00 A; A/B=1-471.
DR PDBsum; 5TL4; -.
DR PDBsum; 5X1I; -.
DR PDBsum; 5X1J; -.
DR PDBsum; 5X1K; -.
DR PDBsum; 5X1L; -.
DR PDBsum; 5X1M; -.
DR PDBsum; 5X1N; -.
DR AlphaFoldDB; G2IQS7; -.
DR SMR; G2IQS7; -.
DR STRING; 627192.SLG_12740; -.
DR EnsemblBacteria; BAK65949; BAK65949; SLG_12740.
DR KEGG; ssy:SLG_12740; -.
DR eggNOG; COG0404; Bacteria.
DR HOGENOM; CLU_046852_1_0_5; -.
DR OrthoDB; 282830at2; -.
DR BRENDA; 2.1.1.341; 7695.
DR UniPathway; UPA00892; -.
DR Proteomes; UP000001275; Chromosome.
DR GO; GO:0008168; F:methyltransferase activity; IEA:UniProtKB-KW.
DR GO; GO:0046274; P:lignin catabolic process; IEA:UniProtKB-UniPathway.
DR GO; GO:0032259; P:methylation; IEA:UniProtKB-KW.
DR Gene3D; 3.30.1360.120; -; 1.
DR InterPro; IPR028896; GCST/YgfZ/DmdA.
DR InterPro; IPR006222; GCV_T_N.
DR InterPro; IPR027266; TrmE/GcvT_dom1.
DR PANTHER; PTHR43757; PTHR43757; 1.
DR Pfam; PF01571; GCV_T; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Lignin degradation; Methyltransferase; Reference proteome;
KW Transferase.
FT CHAIN 1..471
FT /note="Vanillate/3-O-methylgallate O-demethylase"
FT /id="PRO_0000447131"
FT BINDING 31
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:28429420"
FT BINDING 57
FT /ligand="(6S)-5,6,7,8-tetrahydrofolate"
FT /ligand_id="ChEBI:CHEBI:57453"
FT /evidence="ECO:0000269|PubMed:28429420"
FT BINDING 60
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:28429420"
FT BINDING 93
FT /ligand="(6S)-5,6,7,8-tetrahydrofolate"
FT /ligand_id="ChEBI:CHEBI:57453"
FT /evidence="ECO:0000269|PubMed:28429420"
FT BINDING 120
FT /ligand="(6S)-5,6,7,8-tetrahydrofolate"
FT /ligand_id="ChEBI:CHEBI:57453"
FT /evidence="ECO:0000269|PubMed:28429420"
FT BINDING 122
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:28429420"
FT BINDING 165
FT /ligand="(6S)-5,6,7,8-tetrahydrofolate"
FT /ligand_id="ChEBI:CHEBI:57453"
FT /evidence="ECO:0000269|PubMed:28429420"
FT BINDING 215
FT /ligand="(6S)-5,6,7,8-tetrahydrofolate"
FT /ligand_id="ChEBI:CHEBI:57453"
FT /evidence="ECO:0000269|PubMed:28429420"
FT BINDING 247..250
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:28429420"
FT BINDING 256
FT /ligand="(6S)-5,6,7,8-tetrahydrofolate"
FT /ligand_id="ChEBI:CHEBI:57453"
FT /evidence="ECO:0000269|PubMed:28429420"
FT SITE 60
FT /note="Important for activity"
FT /evidence="ECO:0000305|PubMed:28429420"
FT SITE 247
FT /note="Important for activity"
FT /evidence="ECO:0000305|PubMed:28373573,
FT ECO:0000305|PubMed:28429420"
FT MUTAGEN 29
FT /note="Y->A: Almost loss of activity on vanillate."
FT /evidence="ECO:0000269|PubMed:28373573"
FT MUTAGEN 31
FT /note="Y->A: Almost loss or loss of activity on vanillate."
FT /evidence="ECO:0000269|PubMed:28373573,
FT ECO:0000269|PubMed:28429420"
FT MUTAGEN 60
FT /note="H->A: Almost loss or loss of activity on vanillate."
FT /evidence="ECO:0000269|PubMed:28373573,
FT ECO:0000269|PubMed:28429420"
FT MUTAGEN 61
FT /note="M->A: Almost loss of activity on vanillate."
FT /evidence="ECO:0000269|PubMed:28373573"
FT MUTAGEN 62
FT /note="V->A: No change in activity on vanillate."
FT /evidence="ECO:0000269|PubMed:28373573"
FT MUTAGEN 122
FT /note="R->A: Strong decrease in activity on vanillate. Loss
FT of activity on vanillate; when associated with A-147."
FT /evidence="ECO:0000269|PubMed:28373573"
FT MUTAGEN 147
FT /note="R->A: Loss of activity on vanillate; when associated
FT with A-122."
FT /evidence="ECO:0000269|PubMed:28373573"
FT MUTAGEN 247
FT /note="Y->F: Loss of activity on vanillate."
FT /evidence="ECO:0000269|PubMed:28373573,
FT ECO:0000269|PubMed:28429420"
FT CONFLICT 3
FT /note="A -> T (in Ref. 1; BAD61059)"
FT /evidence="ECO:0000305"
FT HELIX 7..13
FT /evidence="ECO:0007829|PDB:5TL4"
FT STRAND 14..16
FT /evidence="ECO:0007829|PDB:5TL4"
FT HELIX 17..22
FT /evidence="ECO:0007829|PDB:5TL4"
FT HELIX 41..50
FT /evidence="ECO:0007829|PDB:5TL4"
FT STRAND 51..56
FT /evidence="ECO:0007829|PDB:5TL4"
FT STRAND 58..68
FT /evidence="ECO:0007829|PDB:5TL4"
FT HELIX 71..78
FT /evidence="ECO:0007829|PDB:5TL4"
FT STRAND 90..94
FT /evidence="ECO:0007829|PDB:5TL4"
FT STRAND 107..113
FT /evidence="ECO:0007829|PDB:5TL4"
FT STRAND 116..121
FT /evidence="ECO:0007829|PDB:5TL4"
FT HELIX 123..135
FT /evidence="ECO:0007829|PDB:5TL4"
FT STRAND 141..145
FT /evidence="ECO:0007829|PDB:5TL4"
FT STRAND 160..168
FT /evidence="ECO:0007829|PDB:5TL4"
FT HELIX 171..179
FT /evidence="ECO:0007829|PDB:5TL4"
FT STRAND 190..196
FT /evidence="ECO:0007829|PDB:5TL4"
FT STRAND 199..206
FT /evidence="ECO:0007829|PDB:5TL4"
FT STRAND 213..219
FT /evidence="ECO:0007829|PDB:5TL4"
FT HELIX 220..222
FT /evidence="ECO:0007829|PDB:5TL4"
FT HELIX 223..234
FT /evidence="ECO:0007829|PDB:5TL4"
FT HELIX 235..237
FT /evidence="ECO:0007829|PDB:5TL4"
FT STRAND 239..242
FT /evidence="ECO:0007829|PDB:5TL4"
FT TURN 244..246
FT /evidence="ECO:0007829|PDB:5TL4"
FT HELIX 247..249
FT /evidence="ECO:0007829|PDB:5TL4"
FT HELIX 250..254
FT /evidence="ECO:0007829|PDB:5TL4"
FT HELIX 268..270
FT /evidence="ECO:0007829|PDB:5TL4"
FT HELIX 271..276
FT /evidence="ECO:0007829|PDB:5TL4"
FT HELIX 282..285
FT /evidence="ECO:0007829|PDB:5TL4"
FT STRAND 288..291
FT /evidence="ECO:0007829|PDB:5TL4"
FT HELIX 297..300
FT /evidence="ECO:0007829|PDB:5TL4"
FT HELIX 304..307
FT /evidence="ECO:0007829|PDB:5TL4"
FT HELIX 310..312
FT /evidence="ECO:0007829|PDB:5TL4"
FT STRAND 315..317
FT /evidence="ECO:0007829|PDB:5X1I"
FT HELIX 322..326
FT /evidence="ECO:0007829|PDB:5TL4"
FT HELIX 330..332
FT /evidence="ECO:0007829|PDB:5TL4"
FT STRAND 335..341
FT /evidence="ECO:0007829|PDB:5TL4"
FT HELIX 343..351
FT /evidence="ECO:0007829|PDB:5TL4"
FT HELIX 352..354
FT /evidence="ECO:0007829|PDB:5TL4"
FT STRAND 367..369
FT /evidence="ECO:0007829|PDB:5TL4"
FT STRAND 373..376
FT /evidence="ECO:0007829|PDB:5TL4"
FT STRAND 378..381
FT /evidence="ECO:0007829|PDB:5TL4"
FT STRAND 387..397
FT /evidence="ECO:0007829|PDB:5TL4"
FT TURN 398..401
FT /evidence="ECO:0007829|PDB:5TL4"
FT STRAND 402..409
FT /evidence="ECO:0007829|PDB:5TL4"
FT STRAND 418..424
FT /evidence="ECO:0007829|PDB:5TL4"
FT HELIX 426..428
FT /evidence="ECO:0007829|PDB:5TL4"
FT STRAND 441..448
FT /evidence="ECO:0007829|PDB:5TL4"
SQ SEQUENCE 471 AA; 52325 MW; 356FE5F4DE55BC6A CRC64;
MSAPTNLEQV LAAGGNTVEM LRNSQIGAYV YPVVAPEFSN WRTEQWAWRN SAVLFDQTHH
MVDLYIRGKD ALKLLSDTMI NSPKGWEPNK AKQYVPVTPY GHVIGDGIIF YLAEEEFVYV
GRAPAANWLM YHAQTGGYNV DIVHDDRSPS RPMGKPVQRI SWRFQIQGPK AWDVIEKLHG
GTLEKLKFFN MAEMNIAGMK IRTLRHGMAG APGLEIWGPY ETQEKARNAI LEAGKEFGLI
PVGSRAYPSN TLESGWIPSP LPAIYTGDKL KAYREWLPAN SYEASGAIGG SFVSSNIEDY
YVNPYEIGYG PFVKFDHDFI GRDALEAIDP ATQRKKVTLA WNGDDMAKIY ASLFDTEADA
HYKFFDLPLA NYANTNADAV LDAAGNVVGM SMFTGYSYNE KRALSLATID HEIPVGTELT
VLWGEENGGT RKTTVEPHKQ MAVRAVVSPV PYSVTARETY EGGWRKAAVT A
