LSDX1_SPHPI
ID LSDX1_SPHPI Reviewed; 485 AA.
AC Q53353;
DT 18-APR-2012, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 63.
DE RecName: Full=Lignostilbene-alpha,beta-dioxygenase isozyme I;
DE Short=LSD-I {ECO:0000303|Ref.4};
DE EC=1.13.11.43 {ECO:0000269|Ref.4};
OS Sphingomonas paucimobilis (Pseudomonas paucimobilis).
OC Bacteria; Proteobacteria; Alphaproteobacteria; Sphingomonadales;
OC Sphingomonadaceae; Sphingomonas.
OX NCBI_TaxID=13689;
RN [1] {ECO:0000305, ECO:0000312|EMBL:AAC60447.2}
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 2-26, FUNCTION,
RP CATALYTIC ACTIVITY, COFACTOR, AND SUBUNIT.
RC STRAIN=TMY1009 {ECO:0000312|EMBL:AAC60447.2};
RX PubMed=7763879; DOI=10.1271/bbb.57.926;
RA Kamoda S., Saburi Y.;
RT "Cloning, expression, and sequence analysis of a lignostilbene-alpha,beta-
RT dioxygenase gene from Pseudomonas paucimobilis TMY1009.";
RL Biosci. Biotechnol. Biochem. 57:926-930(1993).
RN [2] {ECO:0000305}
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND FUNCTION.
RC STRAIN=TMY1009 {ECO:0000269|PubMed:1368688};
RX PubMed=1368688; DOI=10.1271/bbb1961.55.1411;
RA Kamoda S., Samejima M.;
RT "Cloning of a lignostilbene-alpha,beta-dioxygenase gene from Pseudomonas
RT paucimobilis TMY1009.";
RL Agric. Biol. Chem. 55:1411-1412(1991).
RN [3] {ECO:0000305}
RP PROTEIN SEQUENCE OF 2-26, FUNCTION, CATALYTIC ACTIVITY, AND ACTIVITY
RP REGULATION.
RC STRAIN=TMY1009 {ECO:0000269|PubMed:7763880};
RX PubMed=7763880; DOI=10.1271/bbb.57.931;
RA Kamoda S., Saburi Y.;
RT "Structural and enzymatical comparison of lignostilbene-alpha,beta-
RT dioxygenase isozymes, I, II, and III, from Pseudomonas paucimobilis
RT TMY1009.";
RL Biosci. Biotechnol. Biochem. 57:931-934(1993).
RN [4] {ECO:0000305}
RP FUNCTION, CATALYTIC ACTIVITY, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES, AND
RP SUBUNIT.
RC STRAIN=TMY1009 {ECO:0000269|Ref.4};
RX DOI=10.1271/bbb1961.53.2757;
RA Kamoda S., Habu N., Samejima M., Yoshimoto T.;
RT "Purification and some properties of lignostilbene-alpha,beta-dioxygenase
RT responsible for the c-alpha-c-beta cleavage of a diarylpropane type lignin
RT model compound from Pseudomonas sp. TMY1009.";
RL Agric. Biol. Chem. 53:2757-2761(1989).
RN [5] {ECO:0000305}
RP ACTIVITY REGULATION.
RX PubMed=12843670; DOI=10.1271/bbb.67.1394;
RA Kamoda S., Terada T., Saburi Y.;
RT "A common structure of substrate shared by lignostilbenedioxygenase
RT isozymes from Sphingomonas paucimobilis TMY1009.";
RL Biosci. Biotechnol. Biochem. 67:1394-1396(2003).
RN [6] {ECO:0000305}
RP ACTIVITY REGULATION, AND BIOPHYSICOCHEMICAL PROPERTIES.
RX PubMed=14506920; DOI=10.1080/1475636031000080207;
RA Han S.Y., Inoue H., Terada T., Kamoda S., Saburi Y., Sekimata K., Saito T.,
RA Kobayashi M., Shinozaki K., Yoshida S., Asami T.;
RT "N-benzylideneaniline and N-benzylaniline are potent inhibitors of
RT lignostilbene-alpha,beta-dioxygenase, a key enzyme in oxidative cleavage of
RT the central double bond of lignostilbene.";
RL J. Enzym. Inhib. Med. Chem. 18:279-283(2003).
CC -!- FUNCTION: Catalyzes the cleavage of the interphenyl double bond (C
CC alpha-C beta) of lignin-derived polyphenolic diaryl-propane type
CC compounds (Stilbene). {ECO:0000269|PubMed:1368688,
CC ECO:0000269|PubMed:7763879, ECO:0000269|PubMed:7763880,
CC ECO:0000269|Ref.4}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=1,2-bis(4-hydroxy-3-methoxyphenyl)ethylene + O2 = 2 vanillin;
CC Xref=Rhea:RHEA:21340, ChEBI:CHEBI:15379, ChEBI:CHEBI:17501,
CC ChEBI:CHEBI:18346; EC=1.13.11.43;
CC Evidence={ECO:0000269|PubMed:7763879, ECO:0000269|PubMed:7763880,
CC ECO:0000269|Ref.4};
CC -!- COFACTOR:
CC Name=Fe(2+); Xref=ChEBI:CHEBI:29033;
CC Evidence={ECO:0000269|PubMed:7763879, ECO:0000269|Ref.4};
CC Note=1 Fe(2+) ion per subunit. {ECO:0000269|PubMed:7763879,
CC ECO:0000269|Ref.4};
CC -!- ACTIVITY REGULATION: Activity is high with beta-1 type stilbene and
CC minimal with beta-5 type stilbene. A 4-hydroxyl group and trans-
CC stilbene structure is essential for the binding of substrates to the
CC enzyme. Inhibited by N-benzylideneaniline-hydroxy and -methoxy
CC derivatives and N-(4-hydroxybenzyl)-3-methoxyaniline but not N-
CC benzylideneaniline. Fluorinated olefin (Z)-1-fluoro-1(4-hydroxyphenyl)-
CC 2-phenylethylene is also a potent inhibitor. Imine linkage instead of
CC ethylene bridge in the substrate enhances the inhibitory activity.
CC {ECO:0000269|PubMed:12843670, ECO:0000269|PubMed:14506920,
CC ECO:0000269|PubMed:7763880}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=11 uM for 1,2-bis(4-hydroxy-3-methoxyphenyl)-ethylene
CC {ECO:0000269|PubMed:14506920, ECO:0000269|Ref.4};
CC KM=110 uM for oxygen {ECO:0000269|PubMed:14506920,
CC ECO:0000269|Ref.4};
CC KM=8.3 uM for 4-hydroxystilbene {ECO:0000269|PubMed:14506920,
CC ECO:0000269|Ref.4};
CC pH dependence:
CC Optimum pH is 8.5. Active from 5.5-10.5.
CC {ECO:0000269|PubMed:14506920, ECO:0000269|Ref.4};
CC Temperature dependence:
CC Optimum temperature is 30 degrees Celsius. Stable at 4 degrees
CC Celsius with minimal loss of activity. {ECO:0000269|PubMed:14506920,
CC ECO:0000269|Ref.4};
CC -!- SUBUNIT: Homodimer of two alpha subunits. {ECO:0000269|PubMed:7763879,
CC ECO:0000269|Ref.4}.
CC -!- SIMILARITY: Belongs to the carotenoid oxygenase family. {ECO:0000305}.
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DR EMBL; S65040; AAC60447.2; -; Genomic_DNA.
DR PIR; JN0595; JN0595.
DR PDB; 6OJR; X-ray; 2.30 A; A/B=2-483.
DR PDB; 6OJT; X-ray; 3.00 A; A/B=2-482.
DR PDB; 6OJW; X-ray; 2.60 A; A/B=2-481.
DR PDBsum; 6OJR; -.
DR PDBsum; 6OJT; -.
DR PDBsum; 6OJW; -.
DR AlphaFoldDB; Q53353; -.
DR SMR; Q53353; -.
DR BioCyc; MetaCyc:MON-18891; -.
DR GO; GO:0005506; F:iron ion binding; IDA:UniProtKB.
DR GO; GO:0050054; F:lignostilbene alpha beta-dioxygenase activity; IDA:UniProtKB.
DR GO; GO:0046274; P:lignin catabolic process; IDA:UniProtKB.
DR InterPro; IPR004294; Carotenoid_Oase.
DR PANTHER; PTHR10543; PTHR10543; 1.
DR Pfam; PF03055; RPE65; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Dioxygenase; Direct protein sequencing; Iron;
KW Lignin degradation; Metal-binding; Oxidoreductase.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:7763879,
FT ECO:0000269|PubMed:7763880"
FT CHAIN 2..485
FT /note="Lignostilbene-alpha,beta-dioxygenase isozyme I"
FT /evidence="ECO:0000269|PubMed:7763880"
FT /id="PRO_0000416940"
FT BINDING 167
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250"
FT BINDING 218
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250"
FT BINDING 282
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250"
FT BINDING 472
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250"
FT HELIX 8..10
FT /evidence="ECO:0007829|PDB:6OJR"
FT HELIX 12..14
FT /evidence="ECO:0007829|PDB:6OJR"
FT STRAND 20..25
FT /evidence="ECO:0007829|PDB:6OJR"
FT STRAND 27..30
FT /evidence="ECO:0007829|PDB:6OJR"
FT STRAND 37..45
FT /evidence="ECO:0007829|PDB:6OJR"
FT HELIX 58..60
FT /evidence="ECO:0007829|PDB:6OJR"
FT STRAND 63..71
FT /evidence="ECO:0007829|PDB:6OJR"
FT STRAND 74..81
FT /evidence="ECO:0007829|PDB:6OJR"
FT HELIX 85..93
FT /evidence="ECO:0007829|PDB:6OJR"
FT HELIX 104..106
FT /evidence="ECO:0007829|PDB:6OJR"
FT HELIX 109..111
FT /evidence="ECO:0007829|PDB:6OJR"
FT STRAND 121..126
FT /evidence="ECO:0007829|PDB:6OJR"
FT STRAND 129..133
FT /evidence="ECO:0007829|PDB:6OJR"
FT STRAND 139..142
FT /evidence="ECO:0007829|PDB:6OJR"
FT TURN 144..146
FT /evidence="ECO:0007829|PDB:6OJR"
FT STRAND 149..153
FT /evidence="ECO:0007829|PDB:6OJR"
FT TURN 155..158
FT /evidence="ECO:0007829|PDB:6OJR"
FT TURN 172..174
FT /evidence="ECO:0007829|PDB:6OJR"
FT STRAND 177..183
FT /evidence="ECO:0007829|PDB:6OJR"
FT STRAND 191..197
FT /evidence="ECO:0007829|PDB:6OJR"
FT STRAND 203..210
FT /evidence="ECO:0007829|PDB:6OJR"
FT STRAND 212..215
FT /evidence="ECO:0007829|PDB:6OJR"
FT STRAND 224..231
FT /evidence="ECO:0007829|PDB:6OJR"
FT STRAND 234..236
FT /evidence="ECO:0007829|PDB:6OJR"
FT HELIX 238..242
FT /evidence="ECO:0007829|PDB:6OJR"
FT STRAND 247..250
FT /evidence="ECO:0007829|PDB:6OJR"
FT STRAND 252..254
FT /evidence="ECO:0007829|PDB:6OJT"
FT STRAND 256..262
FT /evidence="ECO:0007829|PDB:6OJR"
FT HELIX 267..269
FT /evidence="ECO:0007829|PDB:6OJR"
FT STRAND 271..275
FT /evidence="ECO:0007829|PDB:6OJR"
FT STRAND 285..289
FT /evidence="ECO:0007829|PDB:6OJR"
FT STRAND 292..302
FT /evidence="ECO:0007829|PDB:6OJR"
FT STRAND 311..314
FT /evidence="ECO:0007829|PDB:6OJR"
FT TURN 317..320
FT /evidence="ECO:0007829|PDB:6OJR"
FT STRAND 323..330
FT /evidence="ECO:0007829|PDB:6OJR"
FT STRAND 333..336
FT /evidence="ECO:0007829|PDB:6OJR"
FT STRAND 339..344
FT /evidence="ECO:0007829|PDB:6OJR"
FT STRAND 349..354
FT /evidence="ECO:0007829|PDB:6OJR"
FT HELIX 356..358
FT /evidence="ECO:0007829|PDB:6OJR"
FT STRAND 365..370
FT /evidence="ECO:0007829|PDB:6OJR"
FT STRAND 380..382
FT /evidence="ECO:0007829|PDB:6OJT"
FT STRAND 390..395
FT /evidence="ECO:0007829|PDB:6OJR"
FT TURN 396..398
FT /evidence="ECO:0007829|PDB:6OJR"
FT STRAND 401..405
FT /evidence="ECO:0007829|PDB:6OJR"
FT STRAND 410..412
FT /evidence="ECO:0007829|PDB:6OJR"
FT STRAND 416..421
FT /evidence="ECO:0007829|PDB:6OJR"
FT STRAND 429..437
FT /evidence="ECO:0007829|PDB:6OJR"
FT TURN 438..441
FT /evidence="ECO:0007829|PDB:6OJR"
FT STRAND 442..449
FT /evidence="ECO:0007829|PDB:6OJR"
FT HELIX 453..455
FT /evidence="ECO:0007829|PDB:6OJR"
FT STRAND 458..462
FT /evidence="ECO:0007829|PDB:6OJR"
FT STRAND 473..477
FT /evidence="ECO:0007829|PDB:6OJR"
FT HELIX 478..480
FT /evidence="ECO:0007829|PDB:6OJR"
SQ SEQUENCE 485 AA; 54436 MW; 71A672E375D29A1C CRC64;
MAHFPQTPGF SGTLRPLRIE GDILDIEIEG EVPPQLNGTF HRVHPDAQFP PRFEDDQFFN
GDGMVSLFRF HDGKIDFRQR YAQTDKWKVE RKAGKSLFGA YRNPLTDDAS VQGMIRGTAN
TNVMVHAGKL YAMKEDSPCL IMDPLTLETE GYTNFDGKLQ SQTFCAHPKI DPVTGNLCAF
AYGAKGLMTL DMAYIEISPT GKLLKEIPFQ NPYYCMMHDF GVTEDYAVFA VMPLLSSWDR
LEQRLPFFGF DTTLPCYLGI LPRNGDARDL RWFKTGNCFV GHVMNAFNDG TKVHIDMPVS
RNNSFPFFDV HGAPFDPVAG QGFLTRWTVD MASNGDSFEK TERLFDRPDE FPRIDERYAT
RAYRHGWMLI LDTEKPYEAP GGAFYALTNT LGHIDLATGK SSSWWAGPRC AIQEPCFIPR
SPDAPEGDGY VIALVDDHVA NYSDLAIFDA QHVDQGPIAR AKLPVRIRQG LHGNWADASR
LAVAA
