LIGXA_SPHSK
ID LIGXA_SPHSK Reviewed; 424 AA.
AC G2IN04; Q9ZN84;
DT 10-OCT-2018, integrated into UniProtKB/Swiss-Prot.
DT 16-NOV-2011, sequence version 1.
DT 03-AUG-2022, entry version 49.
DE RecName: Full=5,5'-dehydrodivanillate O-demethylase oxygenase subunit {ECO:0000305};
DE Short=DDVA O-demethylase oxygenase subunit {ECO:0000305};
DE EC=1.14.13.- {ECO:0000269|PubMed:25217011};
GN Name=ligXa {ECO:0000303|PubMed:25217011};
GN Synonyms=ligX {ECO:0000303|PubMed:10788391};
GN ORFNames=SLG_07770 {ECO:0000312|EMBL:BAK65452.1};
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, AND DISRUPTION PHENOTYPE.
RC STRAIN=NBRC 103272 / SYK-6;
RX PubMed=10788391; DOI=10.1128/aem.66.5.2125-2132.2000;
RA Sonoki T., Obi T., Kubota S., Higashi M., Masai E., Katayama Y.;
RT "Coexistence of two different O demethylation systems in lignin metabolism
RT by Sphingomonas paucimobilis SYK-6: cloning and sequencing of the lignin
RT biphenyl-specific O-demethylase (LigX) gene.";
RL Appl. Environ. Microbiol. 66:2125-2132(2000).
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]
RP FUNCTION, CATALYTIC ACTIVITY, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES,
RP SUBUNIT, AND DISRUPTION PHENOTYPE.
RC STRAIN=NBRC 103272 / SYK-6;
RX PubMed=25217011; DOI=10.1128/aem.02236-14;
RA Yoshikata T., Suzuki K., Kamimura N., Namiki M., Hishiyama S., Araki T.,
RA Kasai D., Otsuka Y., Nakamura M., Fukuda M., Katayama Y., Masai E.;
RT "Three-component O-demethylase system essential for catabolism of a lignin-
RT derived biphenyl compound in Sphingobium sp. strain SYK-6.";
RL Appl. Environ. Microbiol. 80:7142-7153(2014).
CC -!- FUNCTION: Involved in the catabolism of 5,5'-dehydrodivanillate (DDVA),
CC an intermediate in the biodegradation of lignin. Part of a three-
CC component monooxygenase that catalyzes the O-demethylation of DDVA,
CC leading to the formation of 2,2',3-trihydroxy-3'-methoxy-5,5'-
CC dicarboxybiphenyl (OH-DDVA). {ECO:0000269|PubMed:10788391,
CC ECO:0000269|PubMed:25217011}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=5,5'-dehydrodivanillate + H(+) + NADH + O2 = 2,2',3-
CC trihydroxy-3'-methoxy-5,5'-dicarboxybiphenyl + formaldehyde + H2O +
CC NAD(+); Xref=Rhea:RHEA:57008, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:15379, ChEBI:CHEBI:16842, ChEBI:CHEBI:57540,
CC ChEBI:CHEBI:57945, ChEBI:CHEBI:141401, ChEBI:CHEBI:141402;
CC Evidence={ECO:0000269|PubMed:25217011};
CC -!- COFACTOR:
CC Name=[2Fe-2S] cluster; Xref=ChEBI:CHEBI:190135;
CC Evidence={ECO:0000255|PROSITE-ProRule:PRU00628};
CC Note=Binds 1 [2Fe-2S] cluster per subunit. {ECO:0000255|PROSITE-
CC ProRule:PRU00628};
CC -!- COFACTOR:
CC Name=Fe cation; Xref=ChEBI:CHEBI:24875;
CC Evidence={ECO:0000250|UniProtKB:F1CMY8, ECO:0000305|PubMed:25217011};
CC Note=Binds 1 Fe cation. {ECO:0000250|UniProtKB:F1CMY8};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC pH dependence:
CC Optimum pH is 6.0. {ECO:0000269|PubMed:25217011};
CC Temperature dependence:
CC Optimum temperature is 25-30 degrees Celsius.
CC {ECO:0000269|PubMed:25217011};
CC -!- SUBUNIT: Homotrimer. The three-component monooxygenase is composed of
CC an oxygenase (LigXa), a ferredoxin (LigXc) and a ferredoxin reductase
CC (LigXd). {ECO:0000269|PubMed:25217011}.
CC -!- DISRUPTION PHENOTYPE: Mutant can degrade syringate and vanillate, but
CC not DDVA. It lacks DDVA O demethylation activity (PubMed:10788391). It
CC cannot grow on minimal medium containing DDVA (PubMed:25217011).
CC {ECO:0000269|PubMed:10788391, ECO:0000269|PubMed:25217011}.
CC -!- SIMILARITY: Belongs to the bacterial ring-hydroxylating dioxygenase
CC alpha subunit family. {ECO:0000305}.
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DR EMBL; AB021319; BAA36168.1; -; Genomic_DNA.
DR EMBL; AP012222; BAK65452.1; -; Genomic_DNA.
DR RefSeq; WP_014075103.1; NC_015976.1.
DR AlphaFoldDB; G2IN04; -.
DR SMR; G2IN04; -.
DR STRING; 627192.SLG_07770; -.
DR EnsemblBacteria; BAK65452; BAK65452; SLG_07770.
DR KEGG; ssy:SLG_07770; -.
DR eggNOG; COG4638; Bacteria.
DR HOGENOM; CLU_039484_2_1_5; -.
DR OrthoDB; 691776at2; -.
DR Proteomes; UP000001275; Chromosome.
DR GO; GO:0051537; F:2 iron, 2 sulfur cluster binding; IEA:UniProtKB-KW.
DR GO; GO:0005506; F:iron ion binding; IEA:InterPro.
DR GO; GO:0004497; F:monooxygenase activity; IEA:UniProtKB-KW.
DR Gene3D; 2.102.10.10; -; 1.
DR InterPro; IPR045623; LigXa_C.
DR InterPro; IPR017941; Rieske_2Fe-2S.
DR InterPro; IPR036922; Rieske_2Fe-2S_sf.
DR InterPro; IPR015881; Ring-hydroxy_dOase_2Fe2S_BS.
DR Pfam; PF19301; LigXa_C; 1.
DR Pfam; PF00355; Rieske; 1.
DR SUPFAM; SSF50022; SSF50022; 1.
DR PROSITE; PS51296; RIESKE; 1.
DR PROSITE; PS00570; RING_HYDROXYL_ALPHA; 1.
PE 1: Evidence at protein level;
KW 2Fe-2S; Iron; Iron-sulfur; Metal-binding; Monooxygenase; NAD;
KW Oxidoreductase; Reference proteome.
FT CHAIN 1..424
FT /note="5,5'-dehydrodivanillate O-demethylase oxygenase
FT subunit"
FT /id="PRO_0000445223"
FT DOMAIN 27..135
FT /note="Rieske"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00628"
FT BINDING 68
FT /ligand="[2Fe-2S] cluster"
FT /ligand_id="ChEBI:CHEBI:190135"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00628"
FT BINDING 70
FT /ligand="[2Fe-2S] cluster"
FT /ligand_id="ChEBI:CHEBI:190135"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00628"
FT BINDING 87
FT /ligand="[2Fe-2S] cluster"
FT /ligand_id="ChEBI:CHEBI:190135"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00628"
FT BINDING 90
FT /ligand="[2Fe-2S] cluster"
FT /ligand_id="ChEBI:CHEBI:190135"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00628"
FT BINDING 181
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000250|UniProtKB:F1CMY8"
FT BINDING 186
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000250|UniProtKB:F1CMY8"
FT BINDING 306
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000250|UniProtKB:F1CMY8"
FT CONFLICT 129..149
FT /note="LGGLLWAYMGPLPAPELPDWE -> WGAFSGPIWAPPRAQTADWA (in
FT Ref. 1; BAA36168)"
FT /evidence="ECO:0000305"
FT CONFLICT 270..302
FT /note="RVPRDAEPYVQESIPVWHGPIKDAQGEWITSHV -> PCRAMPSPMCRSPSP
FT SGMARSRTRKASGSPAM (in Ref. 1; BAA36168)"
FT /evidence="ECO:0000305"
FT CONFLICT 315
FT /note="T -> N (in Ref. 1; BAA36168)"
FT /evidence="ECO:0000305"
FT CONFLICT 357
FT /note="D -> H (in Ref. 1; BAA36168)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 424 AA; 48732 MW; C81744DBCC0D0FF1 CRC64;
MLSAEQNDKL ARVGPGTPMG ELLRRYWHPI GGESEFETKA TRPVRLMGED LVLYKDLSGN
YGLMDRHCPH RRADMACGMV EADGLRCSYH GWMFDAQGAC TEQPFEDTAN PKGRYKDKVR
IKAYPVRALG GLLWAYMGPL PAPELPDWEP FSWKNGFRQI VISVLPCNWL QGQENSMDPI
HFEWMHANWS KRLRGETGPY GPKHLKIDFR EYDYGFTYNR IREDTDETNP LWTIGRACLW
PNAMFTGDHF EYRVPIDDET MMSVGWFFTR VPRDAEPYVQ ESIPVWHGPI KDAQGEWITS
HVMNQDFVAW IGQGTISDRT QENLGLSDKG IGMMRRQFLR DMEKISRGED PKAIIRDPAI
NKAIPLPTIH RDAVMEGMTA EEIEAGGALH LKRFIFQYGQ PEHVLKMQQD AMRISQDNKG
YVDA
