LIGXD_SPHSK
ID LIGXD_SPHSK Reviewed; 412 AA.
AC G2ITT5;
DT 10-OCT-2018, integrated into UniProtKB/Swiss-Prot.
DT 16-NOV-2011, sequence version 1.
DT 03-AUG-2022, entry version 46.
DE RecName: Full=5,5'-dehydrodivanillate O-demethylase ferredoxin reductase subunit {ECO:0000305};
DE Short=DDVA O-demethylase ferredoxin reductase subunit {ECO:0000305};
DE EC=1.14.13.- {ECO:0000269|PubMed:25217011};
GN Name=ligXd {ECO:0000303|PubMed:25217011};
GN ORFNames=SLG_21200 {ECO:0000312|EMBL:BAK66795.1};
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 [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 [2]
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). LigXd probably transfers the electrons
CC from NADH to LigXc. {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=FAD; Xref=ChEBI:CHEBI:57692;
CC Evidence={ECO:0000269|PubMed:25217011};
CC Note=Binds 1 FAD per monomer. {ECO:0000269|PubMed:25217011};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=56 uM for NADH {ECO:0000269|PubMed:25217011};
CC Note=kcat is 538 sec(-1) with NADH as substrate.
CC {ECO:0000269|PubMed:25217011};
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: Monomer. The three-component monooxygenase is composed of an
CC oxygenase (LigXa), a ferredoxin (LigXc) and a ferredoxin reductase
CC (LigXd). {ECO:0000269|PubMed:25217011}.
CC -!- DISRUPTION PHENOTYPE: Disruption mutant shows growth defect on DDVA.
CC {ECO:0000269|PubMed:25217011}.
CC -!- SIMILARITY: Belongs to the FAD-dependent oxidoreductase family.
CC {ECO:0000305}.
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DR EMBL; AP012222; BAK66795.1; -; Genomic_DNA.
DR RefSeq; WP_014076440.1; NC_015976.1.
DR AlphaFoldDB; G2ITT5; -.
DR SMR; G2ITT5; -.
DR STRING; 627192.SLG_21200; -.
DR EnsemblBacteria; BAK66795; BAK66795; SLG_21200.
DR KEGG; ssy:SLG_21200; -.
DR eggNOG; COG1251; Bacteria.
DR HOGENOM; CLU_003291_4_0_5; -.
DR OrthoDB; 1149616at2; -.
DR Proteomes; UP000001275; Chromosome.
DR GO; GO:0050660; F:flavin adenine dinucleotide binding; IEA:InterPro.
DR GO; GO:0004497; F:monooxygenase activity; IEA:UniProtKB-KW.
DR Gene3D; 3.30.390.30; -; 1.
DR Gene3D; 3.50.50.60; -; 2.
DR InterPro; IPR036188; FAD/NAD-bd_sf.
DR InterPro; IPR023753; FAD/NAD-binding_dom.
DR InterPro; IPR016156; FAD/NAD-linked_Rdtase_dimer_sf.
DR InterPro; IPR028202; Reductase_C.
DR Pfam; PF07992; Pyr_redox_2; 1.
DR Pfam; PF14759; Reductase_C; 1.
DR SUPFAM; SSF51905; SSF51905; 2.
DR SUPFAM; SSF55424; SSF55424; 1.
PE 1: Evidence at protein level;
KW FAD; Flavoprotein; Monooxygenase; NAD; Oxidoreductase; Reference proteome.
FT CHAIN 1..412
FT /note="5,5'-dehydrodivanillate O-demethylase ferredoxin
FT reductase subunit"
FT /id="PRO_0000445225"
FT BINDING 14
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250|UniProtKB:P16640"
FT BINDING 49
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250|UniProtKB:P16640"
FT BINDING 82
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250|UniProtKB:P16640"
FT BINDING 130
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250|UniProtKB:P16640"
FT BINDING 279
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250|UniProtKB:P16640"
FT BINDING 298
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250|UniProtKB:P16640"
SQ SEQUENCE 412 AA; 44190 MW; E91312E284BC42F7 CRC64;
MPHFDCLIVG GGHAGAQAAI LLRQLKFEGT VGLISGETEY PYERPPLSKD YLAGEKIFDR
ILLRPRNFWG DQGIELFLGE RVKALQPAEH SLTTASGAEF TYGKLIWAGG GVARRLSCPG
GTAKGLFTVR TRADVDAVMA VLPQAERFAI VGGGYIGLEA AAVLSKLGKQ VTLIEALDRV
LARVAGPELS AFFEDEHRAH GVDVRLACGV EAIEADEQDR ATGVRLADGT IIPTDAVIVG
IGIVPETGPL LLAGASGGNG VDVDEYCLTS LPDVYAIGDC AAHENRFAEG RRVRVESVQN
ANDQARTAVQ HIIGTPAPYD AVPWFWSNQY DLRLQTVGLA VAHDERVVRG DPATRSFSVV
YLRQGHVVAL DCVNRTKDYV QGRALVVDGT RVDRDRLADA DTPLKELTAA QG
