scholarly journals S-Glutathionyl-(chloro)hydroquinone reductases: a novel class of glutathione transferases

2010 ◽  
Vol 428 (3) ◽  
pp. 419-427 ◽  
Author(s):  
Luying Xun ◽  
Sara M. Belchik ◽  
Randy Xun ◽  
Yan Huang ◽  
Huina Zhou ◽  
...  
Keyword(s):  
Disulfide Bond ◽  
Distinct Group ◽  
Degradation Pathway ◽  
Glutathione Transferases ◽  
Amino Acid Residues ◽  
Tblastn Search ◽  
Conserved Domain ◽  
Ping Pong ◽  
Sphingobium Chlorophenolicum ◽  
Domain Database

Sphingobium chlorophenolicum completely mineralizes PCP (pentachlorophenol). Two GSTs (glutathione transferases), PcpC and PcpF, are involved in the degradation. PcpC uses GSH to reduce TeCH (tetrachloro-p-hydroquinone) to TriCH (trichloro-p-hydroquinone) and then to DiCH (dichloro-p-hydroquinone) during PCP degradation. However, oxidatively damaged PcpC produces GS-TriCH (S-glutathionyl-TriCH) and GS-DiCH (S-glutathionyl-TriCH) conjugates. PcpF converts the conjugates into TriCH and DiCH, re-entering the degradation pathway. PcpF was further characterized in the present study. It catalysed GSH-dependent reduction of GS-TriCH via a Ping Pong mechanism. First, PcpF reacted with GS-TriCH to release TriCH and formed disulfide bond between its Cys53 residue and the GS moiety. Then, a GSH came in to regenerate PcpF and release GS–SG. A TBLASTN search revealed that PcpF homologues were widely distributed in bacteria, halobacteria (archaea), fungi and plants, and they belonged to ECM4 (extracellular mutant 4) group COG0435 in the conserved domain database. Phylogenetic analysis grouped PcpF and homologues into a distinct group, separated from Omega class GSTs. The two groups shared conserved amino acid residues, for GSH binding, but had different residues for the binding of the second substrate. Several recombinant PcpF homologues and two human Omega class GSTs were produced in Escherichia coli and purified. They had zero or low activities for transferring GSH to standard substrates, but all had reasonable activities for GSH-dependent reduction of disulfide bond (thiol transfer), dehydroascorbate and dimethylarsinate. All the tested PcpF homologues reduced GS-TriCH, but the two Omega class GSTs did not. Thus PcpF homologues were tentatively named S-glutathionyl-(chloro)hydroquinone reductases for catalysing the GSH-dependent reduction of GS-TriCH.

scholarly journals Maintenance Role of a Glutathionyl-Hydroquinone Lyase (PcpF) in Pentachlorophenol Degradation by Sphingobium chlorophenolicum ATCC 39723

2008 ◽  
Vol 190 (23) ◽  
pp. 7595-7600 ◽  
Author(s):  
Yan Huang ◽  
Randy Xun ◽  
Guanjun Chen ◽  
Luying Xun
Keyword(s):  
Degradation Rate ◽  
Tricarboxylic Acid Cycle ◽  
Degradation Pathway ◽  
Tricarboxylic Acid ◽  
Metabolic Intermediate ◽  
Reductive Dehalogenase ◽  
Cell Extracts ◽  
Toxic Pollutant ◽  
Sphingobium Chlorophenolicum

ABSTRACT Pentachlorophenol (PCP) is a toxic pollutant. Its biodegradation has been extensively studied in Sphingobium chlorophenolicum ATCC 39723. All enzymes required to convert PCP to a common metabolic intermediate before entering the tricarboxylic acid cycle have been characterized. One of the enzymes is tetrachloro-p-hydroquinone (TeCH) reductive dehalogenase (PcpC), which is a glutathione (GSH) S-transferase (GST). PcpC catalyzes the GSH-dependent conversion of TeCH to trichloro-p-hydroquinone (TriCH) and then to dichloro-p-hydroquinone (DiCH) in the PCP degradation pathway. PcpC is susceptible to oxidative damage, and the damaged PcpC produces glutathionyl (GS) conjugates, GS-TriCH and GS-DiCH, which cannot be further metabolized by PcpC. The fate and effect of GS-hydroquinone conjugates were unknown. A putative GST gene (pcpF) is located next to pcpC on the bacterial chromosome. The pcpF gene was cloned, and the recombinant PcpF was purified. The purified PcpF was able to convert GS-TriCH and GS-DiCH conjugates to TriCH and DiCH, respectively. The GS-hydroquinone lyase reactions catalyzed by PcpF are rather unusual for a GST. The disruption of pcpF in S. chlorophenolicum made the mutant lose the GS-hydroquinone lyase activities in the cell extracts. The mutant became more sensitive to PCP toxicity and had a significantly decreased PCP degradation rate, likely due to the accumulation of the GS-hydroquinone conjugates inside the cell. Thus, PcpF played a maintenance role in PCP degradation and converted the GS-hydroquinone conjugates back to the intermediates of the PCP degradation pathway.

scholarly journals Effects of external pH on substrate binding and on the inward chloride translocation rate constant of band 3.

1996 ◽  
Vol 107 (2) ◽  
pp. 271-291 ◽  
Author(s):  
S Q Liu ◽  
F Y Law ◽  
P A Knauf
Keyword(s):  
Rate Constant ◽  
Band 3 ◽  
Complex Model ◽  
Amino Acid Residues ◽  
Ping Pong ◽  
Extracellular Transport ◽  
Charged Form ◽  
Transport Site ◽  
External Ph ◽  
Positively Charged

To test the hypothesis that amino acid residues in band 3 with titratable positive charges play a role in the binding of anions to the outside-facing transport site, we measured the effects of changing external pH (pH(O)) on the dissociation constant for binding of external iodide to the transport site, K(O)(I). K(O)(I) increased with increasing pH(O), and a significant increase was seen even at pH(O) values as low as 9.9. The dependence of K(O)(I) on pH(O) can be explained by a model with one titratable site with pK 9.5 +/- 0.2 (probably lysine), which increases anion affinity for the external transport site when it is in the positively charged form. A more complex model, analogous to one recently proposed by Bjerrum (1992), with two titratable sites, one with pK 9.3 +/- 0.3 (probably lysine) and another with pK > 11 (probably arginine), gives a slightly better fit to the data. Thus, titratable positively charged residues seem to be functionally important for the binding of substrate anions to the outward-facing anion transport site. In addition, analysis of Dixon plot slopes for L inhibition of Cl- exchange at different pH 0 values, coupled with the assumption that pH(O) has parallel effects on external I- and Cl- binding, indicates that k', the rate-constant for inward translocation of the complex of Cl- with the extracellular transport site, decreases with increasing pH(O). The data are compatible with a model in which titration of the pK 9.3 residue decreases k to 14 +/- 10% of its value at neutral pH(O). This result, however, together with Bjerrum's (1992) observation that the maximum flux J(M)) increases 1.6-fold when this residue is deprotonated, makes quantitative predictions that raise significant questions about the adequacy of the two titratable site ping-pong model or the assumptions used in analyzing the data.

scholarly journals CDD: specific functional annotation with the Conserved Domain Database

2009 ◽  
Vol 37 (Database) ◽  
pp. D205-D210 ◽  
Author(s):  
A. Marchler-Bauer ◽  
J. B. Anderson ◽  
F. Chitsaz ◽  
M. K. Derbyshire ◽  
C. DeWeese-Scott ◽  
...  
Keyword(s):  
Functional Annotation ◽  
Conserved Domain ◽  
Domain Database

scholarly journals CDD: a Conserved Domain Database for the functional annotation of proteins

2010 ◽  
Vol 39 (Database) ◽  
pp. D225-D229 ◽  
Author(s):  
A. Marchler-Bauer ◽  
S. Lu ◽  
J. B. Anderson ◽  
F. Chitsaz ◽  
M. K. Derbyshire ◽  
...  
Keyword(s):  
Functional Annotation ◽  
Conserved Domain ◽  
Domain Database

scholarly journals Novel LinA Type 3 δ-Hexachlorocyclohexane Dehydrochlorinase

2015 ◽  
Vol 81 (21) ◽  
pp. 7553-7559 ◽  
Author(s):  
Nidhi Shrivastava ◽  
Zbynek Prokop ◽  
Ashwani Kumar
Keyword(s):  
Amino Acid ◽  
Primary Structure ◽  
Degradation Pathway ◽  
Amino Acid Residues ◽  
Hch Isomers ◽  
New Variant ◽  
Type 3

ABSTRACTLinA is the first enzyme of the microbial degradation pathway of a chlorinated insecticide, hexachlorocyclohexane (HCH), and mediates the dehydrochlorination of α-, γ-, and δ-HCH. Its two variants, LinA type 1 and LinA type 2, which differ at 10 out of 156 amino acid residues, have been described. Their activities for the metabolism of different HCH isomers differ considerably but overall are high for γ-HCH, moderate for α-HCH, low for δ-HCH, and lacking for β-HCH. Here, we describe the characterization of a new variant of this enzyme, LinA type 3, whose gene was identified from the metagenome of an HCH-contaminated soil sample. Its deduced primary structure in the region spanning amino acid residues 1 to 147 of the protein exhibits 17 and 12 differences from LinA type 1 and LinA type 2, respectively. In addition, the residues GIHFAPS, present at the region spanning residues 148 to 154 in both LinA type 1 and LinA type 2, are deleted in LinA type 3.The activity of LinA type 3 for the metabolism of δ-HCH is several orders of magnitude higher than that of LinA type 1 or LinA type 2 and can be useful for improvement of the metabolism of δ-HCH.

scholarly journals NCBI's Conserved Domain Database and Tools for Protein Domain Analysis

2019 ◽  
Vol 69 (1) ◽  
Author(s):  
Mingzhang Yang ◽  
Myra K. Derbyshire ◽  
Roxanne A. Yamashita ◽  
Aron Marchler‐Bauer
Keyword(s):  
Domain Analysis ◽  
Protein Domain ◽  
Conserved Domain ◽  
Domain Database

scholarly journals Organization and Regulation of Pentachlorophenol-Degrading Genes in Sphingobium chlorophenolicum ATCC 39723

2002 ◽  
Vol 184 (17) ◽  
pp. 4672-4680 ◽  
Author(s):  
Mian Cai ◽  
Luying Xun
Keyword(s):  
Transcriptional Regulator ◽  
Degradation Pathway ◽  
Gene Products ◽  
Regulator Gene ◽  
New Genes ◽  
Reductase Gene ◽  
Sphingomonas Chlorophenolica ◽  
Sphingobium Chlorophenolicum ◽  
Maleylacetate Reductase ◽  
Regulator Genes

ABSTRACT The first three enzymes of the pentachlorophenol (PCP) degradation pathway in Sphingobium chlorophenolicum (formerly Sphingomonas chlorophenolica) ATCC 39723 have been characterized, and the corresponding genes, pcpA, pcpB, and pcpC, have been individually cloned and sequenced. To search for new genes involved in PCP degradation and map the physical locations of the pcp genes, a 24-kb fragment containing pcpA and pcpC was completely sequenced. A putative LysR-type transcriptional regulator gene, pcpM, and a maleylacetate reductase gene, pcpE, were identified upstream of pcpA. pcpE was found to play a role in PCP degradation. pcpB was not found on the 24-kb fragment. The four gene products PcpB, PcpC, PcpA, and PcpE were responsible for the metabolism of PCP to 3-oxoadipate in ATCC 39723, and inactivational mutation of each gene disrupted the degradation pathway. The organization of the pcp genes is unusual because the four PCP-degrading genes, pcpA, pcpB, pcpC, and pcpE, were found to be located at four discrete locations. Two hypothetical LysR-type regulator genes, pcpM and pcpR, have been identified; pcpM was not required, but pcpR was essential for the induction of pcpB, pcpA, and pcpE. The coinducers of PcpR were PCP and other polychlorinated phenols. The expression of pcpC was constitutive. Thus, the organization and regulation of the genes involved in PCP degradation to 3-oxoadipate were documented.

scholarly journals Genetic Characterization of the Phenylacetyl-Coenzyme A Oxygenase from the Aerobic Phenylacetic Acid Degradation Pathway of Escherichia coli

2006 ◽  
Vol 72 (11) ◽  
pp. 7422-7426 ◽  
Author(s):  
Cristina Fernández ◽  
Abel Ferrández ◽  
Baltasar Miñambres ◽  
Eduardo Díaz ◽  
José L. García
Keyword(s):  
Escherichia Coli ◽  
Primary Structure ◽  
Phenylacetic Acid ◽  
Coenzyme A ◽  
Genetic Characterization ◽  
Distinct Group ◽  
Degradation Pathway ◽  
Acid Degradation

ABSTRACT We show here that the paaABCDE genes of the paa cluster responsible for phenylacetate degradation in Escherichia coli W encode a five-component oxygenase that hydroxylates phenylacetyl-coenzyme A (CoA), the first intermediate of the pathway. The primary structure of the subunits of bacterial phenylacetyl-CoA oxygenases revealed that these enzymes constitute the prototype of a new and distinct group of the large bacterial diiron multicomponent oxygenase family.

Protein Domain Annotations of the SARS-CoV-2 Proteomics as a Blue-Print for Mapping the Features for Drug and Vaccine Designs

2020 ◽  
Vol 25 (2) ◽  
pp. 26-32
Author(s):  
Arli Parikesit ◽  
Keyword(s):  
Drug Design ◽  
Vaccine Design ◽  
Causal Agent ◽  
Protein Domain ◽  
Potential Drug ◽  
Potential Target ◽  
Conserved Domain ◽  
Drug Lead ◽  
Blue Print ◽  
Domain Database

SARS-CoV-2 virus, as the causal agent for the COVID-19 pandemic, remains an enigma in the bioinformatics sense. Current efforts in drug and vaccine design in primarily targeting general devised protein domain while overlooking the specific features in the proteomics repertoire. However, the NCBI Conserved Domain Database (CDD) could annotate the specific features that are indispensable for a more advanced drug and vaccine design. In this regard, the annotation efforts were initiated with CDD database, and visualized with the 3D Protein Visualizer of Cn3D. The exsistence of the ATP and ADP binding protein with respected domains were found to be a very potential target for drug design. It is recommended that nucleoside inhibitor that could mimick the ATP molecule could serve as a potential drug lead agains SARS-CoV-2.

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