scholarly journals Determinants of specificity for aflatoxin B1-8,9-epoxide in Alpha-class glutathione S-transferases

1999 ◽  
Vol 339 (1) ◽  
pp. 95-101 ◽  
Author(s):  
Paul D. McDONAGH ◽  
David J. JUDAH ◽  
John D. HAYES ◽  
Lu-Yun LIAN ◽  
Gordon E. NEAL ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Substrate Specificity ◽  
High Activity ◽  
Aflatoxin B1 ◽  
Active Site ◽  
Homology Modelling ◽  
Three Dimensional ◽  
Glutathione S Transferase ◽  
Glutathione S Transferases ◽  
Aspartate Residue

We have used homology modelling, based on the crystal structure of the human glutathione S-transferase (GST) A1-1, to obtain the three-dimensional structures of rat GSTA3 and rat GSTA5 subunits bound to S-aflatoxinyl–glutathione. The resulting models highlight two residues, at positions 208 and 108, that could be important for determining, either directly or indirectly, substrate specificity for aflatoxin-exo-8,9-epoxide among the Alpha-class GSTs. Residues at these positions were mutated in human GSTA1-1 (Met-208, Leu-108), rat GSTA3-3 (Glu-208, His-108) and rat GSTA5-5 (Asp-208, Tyr-108): in the active rat GSTA5-5 to those in the inactive GSTA1-1; and in the inactive human GSTA1-1 and rat GSTA3-3 to those in the active rat GSTA5-5. These studies show clearly that, in all three GSTs, an aspartate residue at position 208 is a prerequisite for high activity in aflatoxin-exo-8,9-epoxide conjugation, although this alone is not sufficient; other residues in the vicinity, particularly residues 103–112, are important, perhaps for the optimal orientation of the aflatoxin-exo-8,9-epoxide in the active site for catalysis to occur.

Structural insights into dihydroxylation of terephthalate, a product of polyethylene terephthalate degradation

2022 ◽  
Author(s):  
Jai Krishna Mahto ◽  
Neetu Neetu ◽  
Monica Sharma ◽  
Monika Dubey ◽  
Bhanu Prakash Vellanki ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Substrate Specificity ◽  
Polyethylene Terephthalate ◽  
Active Site ◽  
Catalytic Domain ◽  
Structural Features ◽  
Comamonas Testosteroni ◽  
Plastic Pollution ◽  
Microbial Utilization ◽  
Steady State Kinetics

Biodegradation of terephthalate (TPA) is a highly desired catabolic process for the bacterial utilization of this Polyethylene terephthalate (PET) depolymerization product, but to date, the structure of terephthalate dioxygenase (TPDO), a Rieske oxygenase (RO) that catalyzes the dihydroxylation of TPA to a cis -diol is unavailable. In this study, we characterized the steady-state kinetics and first crystal structure of TPDO from Comamonas testosteroni KF1 (TPDO KF1 ). The TPDO KF1 exhibited the substrate specificity for TPA ( k cat / K m = 57 ± 9 mM −1 s −1 ). The TPDO KF1 structure harbors characteristics RO features as well as a unique catalytic domain that rationalizes the enzyme’s function. The docking and mutagenesis studies reveal that its substrate specificity to TPA is mediated by Arg309 and Arg390 residues, two residues positioned on opposite faces of the active site. Additionally, residue Gln300 is also proven to be crucial for the activity, its substitution to alanine decreases the activity ( k cat ) by 80%. Together, this study delineates the structural features that dictate the substrate recognition and specificity of TPDO. Importance The global plastic pollution has become the most pressing environmental issue. Recent studies on enzymes depolymerizing polyethylene terephthalate plastic into terephthalate (TPA) show some potential in tackling this. Microbial utilization of this released product, TPA is an emerging and promising strategy for waste-to-value creation. Research from the last decade has discovered terephthalate dioxygenase (TPDO), as being responsible for initiating the enzymatic degradation of TPA in a few Gram-negative and Gram-positive bacteria. Here, we have determined the crystal structure of TPDO from Comamonas testosteroni KF1 and revealed that it possesses a unique catalytic domain featuring two basic residues in the active site to recognize TPA. Biochemical and mutagenesis studies demonstrated the crucial residues responsible for the substrate specificity of this enzyme.

scholarly journals The three-dimensional structure of a class-Pi glutathione S-transferase complexed with glutathione: the active-site hydration provides insights into the reaction mechanism

1998 ◽  
Vol 333 (3) ◽  
pp. 811-816 ◽  
Author(s):  
Antonio PÁRRAGA ◽  
Isabel GARCÍA-SÁEZ ◽  
Sinead B. WALSH ◽  
Timothy J. MANTLE ◽  
Miquel COLL
Keyword(s):  
Conformational Changes ◽  
Active Site ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Water Molecules ◽  
X Ray Diffraction ◽  
Glutathione S Transferase ◽  
X Ray ◽  
The Right

The structure of mouse liver glutathione S-transferase P1-1 complexed with its substrate glutathione (GSH) has been determined by X-ray diffraction analysis. No conformational changes in the glutathione moiety or in the protein, other than small adjustments of some side chains, are observed when compared with glutathione adduct complexes. Our structure confirms that the role of Tyr-7 is to stabilize the thiolate by hydrogen bonding and to position it in the right orientation. A comparison of the enzyme–GSH structure reported here with previously described structures reveals rearrangements in a well-defined network of water molecules in the active site. One of these water molecules (W0), identified in the unliganded enzyme (carboxymethylated at Cys-47), is displaced by the binding of GSH, and a further water molecule (W4) is displaced following the binding of the electrophilic substrate and the formation of the glutathione conjugate. The possibility that one of these water molecules participates in the proton abstraction from the glutathione thiol is discussed.

scholarly journals The presence and longitudinal distribution of the glutathione S-transferase in rat epididymis and vas deferens

1980 ◽  
Vol 189 (1) ◽  
pp. 135-142 ◽  
Author(s):  
Barbara F. Hales ◽  
Christiane Hachey ◽  
Bernard Robaire
Keyword(s):  
Substrate Specificity ◽  
Isoelectric Focusing ◽  
Vas Deferens ◽  
Longitudinal Distribution ◽  
Transferase Activity ◽  
Glutathione S Transferase ◽  
Potential Significance ◽  
Glutathione S Transferases ◽  
Rat Epididymis ◽  
First Time

The presence of the glutathione S-transferases, enzymes that catalyse the conjugation of glutathione with a variety of compounds, is reported here, for the first time, in the mammalian epididymis–vas deferens. These glutathione S-transferases, approx. 50% of those from rat liver on a per-mg-of-protein basis, are resolved by isoelectric focusing into six peaks, each with a characteristic isoelectric point and substrate specificity. By these same criteria, the first three peaks (pI 8.9, 8.2 and 7.8) can be identified as transferases B, A and C respectively. The fifth peak (pI7.2) may correspond to transferase M; the fourth (pI7.5) and sixth (pI7.0) peaks do not correspond to previously described transferases. The distribution of transferase activity towards any one substrate studied differs in sequential sections of the epididymis and vas deferens; in addition, the longitudinal-distribution pattern differs for each of the three substrates studied. Isoelectric focusing of the cytosol fractions of the different sections further substantiates these observations. The potential significance of these enzymes and of their distribution in terms of epididymal function, maturation of spermatozoa, is discussed.

Computational and functional analysis of β-lactam resistance in Zymomonas mobilis

Biologia ◽  
2013 ◽  
Vol 68 (6) ◽  
Author(s):  
Sheik Sheik Abdul Kader ◽  
Mahalakshmi Ayyasamy ◽  
Rajnish Narayanan ◽  
Sridhar Jayavel ◽  
Gunasekaran Paramasamy
Keyword(s):  
Substrate Specificity ◽  
Zymomonas Mobilis ◽  
Homology Modelling ◽  
Three Dimensional ◽  
Docking Studies ◽  
Pcr Analysis ◽  
Resistance Determinants ◽  
Disk Diffusion Assay ◽  
Aliphatic Index ◽  
High Concentrations

AbstractZymomonas mobilis, a Gram-negative ethanologenic non-pathogenic bacterium, is reported to exhibit resistance to high concentrations of β-lactam antibiotics. In the present study, Z. mobilis was found to be resistant to I-IV generations of cephalosporins and carbapenems, i.e. narrow, broad and extended spectrum β-lactam antibiotics. We have analysed the genome of Z. mobilis (GenBank accession No.: NC 006526) harbouring multiple genes coding for β-lactamases (BLA), β-lactamase domain containing proteins (BDP) and penicillin binding proteins (PBP). The conserved domain database analysis of BDPs predicted them to be members of metallo β-lactamase superfamily. Further, class C specific multidomain AmpC (β-lactamase C) was found in the three β-lactamases. The β-lactam resistance determinants motifs, HXHXD, KXG, SXXK, SXN, and YXN are present in the BLAs, BDPs and PBPs of Z. mobilis. The predicted theoretical pI and aliphatic index values suggested their stability. One of the PBPs, PBP2, was predicted to share functional association with rod shape determining proteins (GenBank accession Nos. YP_162095 and YP_162091). Homology modelling of three dimensional structures of the β-lactam resistance determinants and further docking studies with penicillin and other β-lactam antibiotics indicated their substrate-specificity. Semi-quantitative PCR analysis indicated that the expression of all BLAs and one BDP are induced by penicillin. Disk diffusion assay, SDS-PAGE and zymogram analysis confirms the substrate specificity of the β-lactam resistance determinants. This study gives a broader picture of the β-lactam resistance determinants of a non-pathogenic ethanologenic Z. mobilis bacterium that could have implications in laboratories since it is routinely used in many research laboratories in the world for ethanol, fructooligosaccharides, levan production and has also been reported to be present in wine and beer as a spoilage organism.

Free and ATP-bound structures of Ap4A hydrolase fromAquifex aeolicusV5

2010 ◽  
Vol 66 (2) ◽  
pp. 116-124 ◽  
Author(s):  
Jeyaraman Jeyakanthan ◽  
Shankar Prasad Kanaujia ◽  
Yuya Nishida ◽  
Noriko Nakagawa ◽  
Surendran Praveen ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Conformational Changes ◽  
Active Site ◽  
Three Dimensional ◽  
Protein Molecule ◽  
Water Molecules ◽  
Aquifex Aeolicus ◽  
Functional Roles ◽  
Product Molecule ◽  
Dimensional Crystal

Asymmetric diadenosine tetraphosphate (Ap4A) hydrolases degrade the metabolite Ap4A back into ATP and AMP. The three-dimensional crystal structure of Ap4A hydrolase (16 kDa) fromAquifex aeolicushas been determined in free and ATP-bound forms at 1.8 and 1.95 Å resolution, respectively. The overall three-dimensional crystal structure of the enzyme shows an αβα-sandwich architecture with a characteristic loop adjacent to the catalytic site of the protein molecule. The ATP molecule is bound in the primary active site and the adenine moiety of the nucleotide binds in a ring-stacking arrangement equivalent to that observed in the X-ray structure of Ap4A hydrolase fromCaenorhabditis elegans. Binding of ATP in the active site induces local conformational changes which may have important implications in the mechanism of substrate recognition in this class of enzymes. Furthermore, two invariant water molecules have been identified and their possible structural and/or functional roles are discussed. In addition, modelling of the substrate molecule at the primary active site of the enzyme suggests a possible path for entry and/or exit of the substrate and/or product molecule.

Homology modelling and structural analysis of human arylamine N-acetyltransferase NAT1: evidence for the conservation of a cysteine protease catalytic domain and an active-site loop

2001 ◽  
Vol 356 (2) ◽  
pp. 327-334 ◽  
Author(s):  
Fernando RODRIGUES-LIMA ◽  
Claudine DELOMÉNIE ◽  
Geoffrey H. GOODFELLOW ◽  
Denis M. GRANT ◽  
Jean-Marie DUPRET
Keyword(s):  
Crystal Structure ◽  
Cysteine Protease ◽  
Active Site ◽  
Catalytic Mechanism ◽  
Catalytic Domain ◽  
Homology Modelling ◽  
Metabolic Activation ◽  
Cysteine Proteases ◽  
Catalytic Triad ◽  
Quality Model

Arylamine N-acetyltransferases (EC 2.3.1.5) (NATs) catalyse the biotransformation of many primary arylamines, hydrazines and their N-hydroxylated metabolites, thereby playing an important role in both the detoxification and metabolic activation of numerous xenobiotics. The recently published crystal structure of the Salmonella typhimurium NAT (StNAT) revealed the existence of a cysteine protease-like (Cys-His-Asp) catalytic triad. In the present study, a three-dimensional homology model of human NAT1, based upon the crystal structure of StNAT [Sinclair, Sandy, Delgoda, Sim and Noble (2000) Nat. Struct. Biol. 7, 560–564], is demonstrated. Alignment of StNAT and NAT1, together with secondary structure predictions, have defined a consensus region (residues 29–131) in which 37% of the residues are conserved. Homology modelling provided a good quality model of the corresponding region in human NAT1. The location of the catalytic triad was found to be identical in StNAT and NAT1. Comparison of active-site structural elements revealed that a similar length loop is conserved in both species (residues 122–131 in NAT1 model and residues 122–133 in StNAT). This observation may explain the involvement of residues 125, 127 and 129 in human NAT substrate selectivity. Our model, and the fact that cysteine protease inhibitors do not affect the activity of NAT1, suggests that human NATs may have adapted a common catalytic mechanism from cysteine proteases to accommodate it for acetyl-transfer reactions.

scholarly journals Ethoxyquin-induced resistance to aflatoxin B1 in the rat is associated with the expression of a novel Alpha-class glutathione S-transferase subunit, Yc2, which possesses high catalytic activity for aflatoxin B1-8,9-epoxide

1991 ◽  
Vol 279 (2) ◽  
pp. 385-398 ◽  
Author(s):  
J D Hayes ◽  
D J Judah ◽  
L I McLellan ◽  
L A Kerr ◽  
S D Peacock ◽  
...  
Keyword(s):  
Aflatoxin B1 ◽  
Neonatal Rat ◽  
High Catalytic Activity ◽  
Amino Acid Sequencing ◽  
Glutathione S Transferase ◽  
Adult Rats ◽  
Purification Scheme ◽  
Glutathione S Transferases ◽  
A Subunit ◽  
Rat Livers

A purification scheme has been devised for two ethoxyquin-inducible Alpha-class glutathione S-transferases (GSTs) which possess at least 25-fold greater activity towards aflatoxin B1 (AFB1)-8,9-epoxide than that exhibited by the GSTs (i.e. F, L, B and AA) that have been described previously. These two enzymes are both heterodimers and both contain a subunit of Mr 25,800. This subunit has been isolated from both of the GST isoenzymes and, after cleavage with CNBr, it has been subjected to automated amino acid sequencing. The primary structure of the Mr 25,800 subunit revealed that it forms part of a subfamily of Alpha-class GSTs which possess closest identity (about 92%) with the Yc subunit of apparent Mr 27,500, which is encoded by the recombinant cDNA clone pGTB42 [Telakowski-Hopkins, Rodkey, Bennett, Lu & Pickett (1985) J. Biol. Chem. 260, 5820-5825]. As these two GSTs possess less than 70% sequence identity with the Ya1 and Ya2 subunits, both of Mr 25,500, the constitutively expressed Yc subunit of Mr 27,500 has been renamed Yc1 and the ethoxyquin-inducible GST of Mr 25,800 has been designated Yc2. Using this nomenclature, the two GSTs with high activity for AFB1-8,9-epoxide are Ya1Yc2 and Yc1Yc2. Although evidence suggests that induction of Yc2 is responsible for the high detoxification capacity of livers from ethoxyquin-treated rats for AFB1-8,9-epoxide, resistance towards AFB1 may be multifactorial in this instance as dietary ethoxyquin also induces the Ya1, Ya2 and Yc1 subunits about 2.2-, 10.9- and 2.7-fold respectively. Besides the induction of GST by ethoxyquin, activity towards AFB1-8,9-epoxide is also elevated in the livers of neonatal rats and in livers that contain preneoplastic nodules. Western blotting experiments show that Yc2 is not present in hepatic cytosol from adult rats fed on normal diets but is expressed in neonatal rat livers and in the livers of adult rats that contain preneoplastic nodules that have arisen as a consequence of consuming diets contaminated with AFB1.

scholarly journals Structure and function of one unclassified-class glutathione S-transferase in Leptinotarsa decemlineata

2021 ◽  
Author(s):  
Yanjun Liu ◽  
Timothy W Moural ◽  
Sonu BK Koirala ◽  
Jonathan Hernandez ◽  
Zhongjian Shen ◽  
...  
Keyword(s):  
Kinetic Parameters ◽  
Three Dimensional ◽  
Large Family ◽  
Dimensional Structure ◽  
Glutathione S Transferase ◽  
X Ray Crystallography ◽  
Xenobiotic Exposure ◽  
Multifunctional Enzymes ◽  
Glutathione S Transferases ◽  
And Function

Arthropod Glutathione S-transferases (GSTs) constitute a large family of multifunctional enzymes that are mainly associated with xenobiotic or stress adaptation. GST-mediated xenobiotic adaptation is through direct metabolism or sequestration of xenobiotics, and/or indirectly by providing protection against oxidative stress induced by xenobiotic exposure. To date, the roles of GSTs in xenobiotic adaptation in the Colorado potato beetle (CPB), a notorious agriculture pest of plants within Solanaceae have not been well studied. Here, we functionally expressed and characterized an unclassified-class GST, LdGSTu1. The three-dimensional structure of the LdGSTu1 was solved with a resolution up to 1.8 Å by x-ray crystallography. Recombinant LdGSTu1 was used to determine enzyme activity and kinetic parameters using 1-chloro-2,4-dinitrobenzene (CDNB), GSH, p-nitrophenyl acetate (PNA) as substrates. The enzyme kinetic parameters and enzyme-substrate interaction studies demonstrated that LdGSTu1 could catalyze the conjugation of GSH to both CDNB and PNA, with a higher turnover number for CDNB than PNA. The LdGSTu1 enzyme inhibition assays demonstrated that the enzymatic conjugation of GSH to CDNB could be inhibited by multiple pesticides, suggesting a potential function of LdGSTu1 in xenobiotic adaptation.

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