PCPD_SPHCR
ID PCPD_SPHCR Reviewed; 324 AA.
AC Q47914;
DT 20-JUN-2018, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2002, sequence version 2.
DT 03-AUG-2022, entry version 126.
DE RecName: Full=Tetrachlorobenzoquinone reductase {ECO:0000303|PubMed:23676275};
DE Short=TCBQ reductase {ECO:0000303|PubMed:23676275};
DE EC=1.1.1.404 {ECO:0000269|PubMed:19325743, ECO:0000269|PubMed:23676275};
GN Name=pcpD {ECO:0000303|PubMed:23676275};
OS Sphingobium chlorophenolicum.
OC Bacteria; Proteobacteria; Alphaproteobacteria; Sphingomonadales;
OC Sphingomonadaceae; Sphingobium.
OX NCBI_TaxID=46429;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-187.
RC STRAIN=ATCC 39723 / DSM 6824 / L-1 {ECO:0000312|EMBL:AAA68938.2};
RX PubMed=7678243; DOI=10.1128/jb.175.2.411-416.1993;
RA Orser C.S., Lange C.C., Xun L., Zahrt T.C., Schneider B.J.;
RT "Cloning, sequence analysis, and expression of the Flavobacterium
RT pentachlorophenol-4-monooxygenase gene in Escherichia coli.";
RL J. Bacteriol. 175:411-416(1993).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 39723 / DSM 6824 / L-1 {ECO:0000312|EMBL:AAA68938.2};
RX PubMed=12169590; DOI=10.1128/jb.184.17.4672-4680.2002;
RA Cai M., Xun L.;
RT "Organization and regulation of pentachlorophenol-degrading genes in
RT Sphingobium chlorophenolicum ATCC 39723.";
RL J. Bacteriol. 184:4672-4680(2002).
RN [3]
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, COFACTOR,
RP PATHWAY, SUBUNIT, ACTIVITY REGULATION, AND INDUCTION.
RC STRAIN=ATCC 39723 / DSM 6824 / L-1;
RX PubMed=19325743; DOI=10.3390/ijms9030198;
RA Chen L., Yang J.;
RT "Biochemical characterization of the tetrachlorobenzoquinone reductase
RT involved in the biodegradation of pentachlorophenol.";
RL Int. J. Mol. Sci. 9:198-212(2008).
RN [4]
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, COFACTOR,
RP PATHWAY, SUBUNIT, DISRUPTION PHENOTYPE, AND SUBSTRATE SPECIFICITY.
RC STRAIN=ATCC 39723 / DSM 6824 / L-1;
RX PubMed=23676275; DOI=10.1073/pnas.1214052110;
RA Yadid I., Rudolph J., Hlouchova K., Copley S.D.;
RT "Sequestration of a highly reactive intermediate in an evolving pathway for
RT degradation of pentachlorophenol.";
RL Proc. Natl. Acad. Sci. U.S.A. 110:E2182-E2190(2013).
CC -!- FUNCTION: Involved in the degradation of the xenobiocide
CC pentachlorophenol (PCP) (PubMed:19325743, PubMed:23676275). Catalyzes
CC the reduction of tetrachlorobenzoquinone (TCBQ) to yield
CC tetrachlorohydroquinone (TCHQ) (PubMed:19325743, PubMed:23676275). Also
CC able to reduce 2,6-dichloroindophenol (DCIP) (PubMed:23676275).
CC {ECO:0000269|PubMed:19325743, ECO:0000269|PubMed:23676275}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2,3,5,6-tetrachlorohydroquinone + H(+) + NAD(+) = 2,3,5,6-
CC tetrachloro-1,4-benzoquinone + NADH; Xref=Rhea:RHEA:51888,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:36703, ChEBI:CHEBI:57540,
CC ChEBI:CHEBI:57945, ChEBI:CHEBI:57994; EC=1.1.1.404;
CC Evidence={ECO:0000269|PubMed:19325743, ECO:0000269|PubMed:23676275};
CC -!- COFACTOR:
CC Name=FMN; Xref=ChEBI:CHEBI:58210;
CC Evidence={ECO:0000269|PubMed:23676275, ECO:0000305|PubMed:19325743};
CC -!- COFACTOR:
CC Name=[2Fe-2S] cluster; Xref=ChEBI:CHEBI:190135;
CC Evidence={ECO:0000269|PubMed:19325743, ECO:0000269|PubMed:23676275};
CC Note=Binds 1 [2Fe-2S] cluster. {ECO:0000269|PubMed:19325743};
CC -!- ACTIVITY REGULATION: In vitro, activated by tetrachlorohydroquinone
CC (TCHQ) at low concentrations and inhibited at high concentrations
CC (above 200 uM). However, PcpD would only be stimulated by
CC tetrachlorohydroquinone (TCHQ) under in vivo conditions due to the
CC toxicity of tetrachlorohydroquinone (TCHQ). Competitively inhibited by
CC pentachlorophenol (PCP) in a concentration-dependent manner. PcpD is
CC regulated by tetrachlorohydroquinone (TCHQ) and pentachlorophenol (PCP)
CC using a mechanism, which maintains tetrachlorobenzoquinone at a level
CC that would neither significantly decrease the biodegradation of
CC pentachlorophenol (PCP) nor cause cytotoxicity in cells.
CC {ECO:0000269|PubMed:19325743}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=1.21 uM for NADPH (with 90 uM cytochrome c)
CC {ECO:0000269|PubMed:23676275};
CC KM=11.5 uM for NADH (with 90 uM cytochrome c)
CC {ECO:0000269|PubMed:23676275};
CC KM=17.6 uM for cytochrome c (with 100 uM NADH)
CC {ECO:0000269|PubMed:23676275};
CC KM=38.3 uM for 2,6-dichloroindophenol (DCIP) (with 100 uM NADH)
CC {ECO:0000269|PubMed:23676275};
CC Note=kcat is 20.1 sec(-1) for NADH as substrate (with 90 uM
CC cytochrome c). kcat is 14.1 sec(-1) for 2,6-dichloroindophenol (DCIP)
CC as substrate (with 100 uM NADH). kcat is 9.1 sec(-1) for cytochrome c
CC as substrate (with 100 uM NADH). kcat is 3.7 sec(-1) for NADPH as
CC substrate (with 90 uM cytochrome c). {ECO:0000269|PubMed:23676275};
CC pH dependence:
CC Optimum pH is 7. It maintains more than 70% of its optimal activity
CC even at pH 5.0. PcpD loses its activity quickly in basic solutions,
CC retaining less than 20% of its optimal activity at pH 8.0.
CC {ECO:0000269|PubMed:19325743};
CC -!- PATHWAY: Xenobiotic degradation; pentachlorophenol degradation.
CC {ECO:0000269|PubMed:23676275, ECO:0000305|PubMed:19325743}.
CC -!- SUBUNIT: Homotrimer. {ECO:0000269|PubMed:19325743,
CC ECO:0000269|PubMed:23676275}.
CC -!- INDUCTION: Constitutively expressed. {ECO:0000269|PubMed:19325743}.
CC -!- DISRUPTION PHENOTYPE: Cells lacking this gene show a significant
CC sensitivity to pentachlorophenol (PCP) and 2,4,6-trichlorophenol
CC (TriCP). {ECO:0000269|PubMed:23676275}.
CC -!- SIMILARITY: Belongs to the PDR/VanB family. {ECO:0000305}.
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DR EMBL; U12290; AAA68938.2; -; Genomic_DNA.
DR AlphaFoldDB; Q47914; -.
DR SMR; Q47914; -.
DR BRENDA; 1.1.1.404; 7700.
DR UniPathway; UPA00691; -.
DR GO; GO:0051537; F:2 iron, 2 sulfur cluster binding; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0016491; F:oxidoreductase activity; IEA:UniProtKB-KW.
DR GO; GO:0019338; P:pentachlorophenol catabolic process; IEA:UniProtKB-UniPathway.
DR CDD; cd00207; fer2; 1.
DR Gene3D; 3.10.20.30; -; 1.
DR Gene3D; 3.40.50.80; -; 1.
DR InterPro; IPR036010; 2Fe-2S_ferredoxin-like_sf.
DR InterPro; IPR001041; 2Fe-2S_ferredoxin-type.
DR InterPro; IPR006058; 2Fe2S_fd_BS.
DR InterPro; IPR012675; Beta-grasp_dom_sf.
DR InterPro; IPR017927; FAD-bd_FR_type.
DR InterPro; IPR039261; FNR_nucleotide-bd.
DR InterPro; IPR001433; OxRdtase_FAD/NAD-bd.
DR InterPro; IPR000951; Ph_dOase_redase.
DR InterPro; IPR017938; Riboflavin_synthase-like_b-brl.
DR Pfam; PF00111; Fer2; 1.
DR Pfam; PF00175; NAD_binding_1; 1.
DR PRINTS; PR00409; PHDIOXRDTASE.
DR SUPFAM; SSF52343; SSF52343; 1.
DR SUPFAM; SSF54292; SSF54292; 1.
DR SUPFAM; SSF63380; SSF63380; 1.
DR PROSITE; PS00197; 2FE2S_FER_1; 1.
DR PROSITE; PS51085; 2FE2S_FER_2; 1.
DR PROSITE; PS51384; FAD_FR; 1.
PE 1: Evidence at protein level;
KW 2Fe-2S; Aromatic hydrocarbons catabolism; Electron transport; Flavoprotein;
KW FMN; Iron; Iron-sulfur; Metal-binding; NAD; Oxidoreductase; Transport.
FT CHAIN 1..324
FT /note="Tetrachlorobenzoquinone reductase"
FT /id="PRO_0000444444"
FT DOMAIN 5..107
FT /note="FAD-binding FR-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00716"
FT DOMAIN 238..324
FT /note="2Fe-2S ferredoxin-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00465"
FT BINDING 273
FT /ligand="[2Fe-2S] cluster"
FT /ligand_id="ChEBI:CHEBI:190135"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00465"
FT BINDING 278
FT /ligand="[2Fe-2S] cluster"
FT /ligand_id="ChEBI:CHEBI:190135"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00465"
FT BINDING 281
FT /ligand="[2Fe-2S] cluster"
FT /ligand_id="ChEBI:CHEBI:190135"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00465"
FT BINDING 311
FT /ligand="[2Fe-2S] cluster"
FT /ligand_id="ChEBI:CHEBI:190135"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00465"
SQ SEQUENCE 324 AA; 35598 MW; 1FADB899AECC90AE CRC64;
MTNPVSTIDM TVTQITRVAK DINSYELRPE PGVILPEFTA GAHIGVSLPN GIQRSYSLVN
PQGERDRYVI TVNLDRNSRG GSRYLHEQLR VGQRLSIVPP ANNFALVETA PHSVLFAGGI
GITPIWSMIQ RLRELGSTWE LHYACRGKDF VAYRQELEQA AAEAGARFHL HLDEEADGKF
LDLAGPVAQA GQDSIFYCCG PEAMLQAYKA ATADLPSERV RFEHFGAALT GEPADDVFTV
VLARRSGQEF TVEPGMTILE TLLQNGISRN YSCTQGVCGT CETKVLEGEP DHRDWVLSDE
KKASNSTMLI CCSLSKSPRL VLDI
