Theoretical insights into the reaction and inhibition mechanism of metal-independent retaining glycosyltransferase responsible for mycothiol biosynthesis
Understanding enzymatic reactions with atomic resolution has proven in recent years to be of tremendous interest for biochemical research, and thus, the use of QM/MM methods for the study of reaction mechanisms is experiencing a continuous growth. Glycosyltransferases (GTs) catalyze the formation of...
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todo:paper_15206106_v121_n3_p471_Capurro2023-10-03T16:20:32Z Theoretical insights into the reaction and inhibition mechanism of metal-independent retaining glycosyltransferase responsible for mycothiol biosynthesis Capurro, J.I.B. Hopkins, C.W. Sottile, G.P. González Lebrero, M.C. Roitberg, A.E. Marti, M.A. Biosynthesis Electronic structure Enzymes Free energy Biochemical research Concerted reactions Enzymatic reaction Glycosyl transferase Glycosyltransferases Inhibition mechanisms Mycobacterium tuberculosis Reaction mechanism Biochemistry amidase bacterial protein cysteine glycopeptide glycosyltransferase inositol metal mycothiol N-acetyl-1-D-inosityl-2-amino-2-deoxy-alpha-D-glucopyranoside deacetylase antagonists and inhibitors biocatalysis biosynthesis chemistry metabolism Mycobacterium tuberculosis quantum theory Amidohydrolases Bacterial Proteins Biocatalysis Cysteine Glycopeptides Glycosyltransferases Inositol Metals Mycobacterium tuberculosis Quantum Theory Understanding enzymatic reactions with atomic resolution has proven in recent years to be of tremendous interest for biochemical research, and thus, the use of QM/MM methods for the study of reaction mechanisms is experiencing a continuous growth. Glycosyltransferases (GTs) catalyze the formation of glycosidic bonds, and are important for many biotechnological purposes, including drug targeting. Their reaction product may result with only one of the two possible stereochemical outcomes for the reacting anomeric center, and therefore, they are classified as either inverting or retaining GTs. While the inverting GT reaction mechanism has been widely studied, the retaining GT mechanism has always been controversial and several questions remain open to this day. In this work, we take advantage of our recent GPU implementation of a pure QM(DFT-PBE)/MM approach to explore the reaction and inhibition mechanism of MshA, a key retaining GT responsible for the first step of mycothiol biosynthesis, a low weight thiol compound found in pathogens like Mycobacterium tuberculosis that is essential for its survival under oxidative stress conditions. Our results show that the reaction proceeds via a front-side SNi-like concerted reaction mechanism (DNAN in IUPAC nomenclature) and has a 17.5 kcal/mol free energy barrier, which is in remarkable agreement with experimental data. Detailed analysis shows that the key reaction step is the diphosphate leaving group dissociation, leading to an oxocarbenium-ion-like transition state. In contrast, fluorinated substrate analogues increase the reaction barrier significantly, rendering the enzyme effectively inactive. Detailed analysis of the electronic structure along the reaction suggests that this particular inhibition mechanism is associated with fluorine's high electronegative nature, which hinders phosphate release and proper stabilization of the transition state. © 2016 American Chemical Society. JOUR info:eu-repo/semantics/openAccess http://creativecommons.org/licenses/by/2.5/ar http://hdl.handle.net/20.500.12110/paper_15206106_v121_n3_p471_Capurro |
| institution |
Universidad de Buenos Aires |
| institution_str |
I-28 |
| repository_str |
R-134 |
| collection |
Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA) |
| topic |
Biosynthesis Electronic structure Enzymes Free energy Biochemical research Concerted reactions Enzymatic reaction Glycosyl transferase Glycosyltransferases Inhibition mechanisms Mycobacterium tuberculosis Reaction mechanism Biochemistry amidase bacterial protein cysteine glycopeptide glycosyltransferase inositol metal mycothiol N-acetyl-1-D-inosityl-2-amino-2-deoxy-alpha-D-glucopyranoside deacetylase antagonists and inhibitors biocatalysis biosynthesis chemistry metabolism Mycobacterium tuberculosis quantum theory Amidohydrolases Bacterial Proteins Biocatalysis Cysteine Glycopeptides Glycosyltransferases Inositol Metals Mycobacterium tuberculosis Quantum Theory |
| spellingShingle |
Biosynthesis Electronic structure Enzymes Free energy Biochemical research Concerted reactions Enzymatic reaction Glycosyl transferase Glycosyltransferases Inhibition mechanisms Mycobacterium tuberculosis Reaction mechanism Biochemistry amidase bacterial protein cysteine glycopeptide glycosyltransferase inositol metal mycothiol N-acetyl-1-D-inosityl-2-amino-2-deoxy-alpha-D-glucopyranoside deacetylase antagonists and inhibitors biocatalysis biosynthesis chemistry metabolism Mycobacterium tuberculosis quantum theory Amidohydrolases Bacterial Proteins Biocatalysis Cysteine Glycopeptides Glycosyltransferases Inositol Metals Mycobacterium tuberculosis Quantum Theory Capurro, J.I.B. Hopkins, C.W. Sottile, G.P. González Lebrero, M.C. Roitberg, A.E. Marti, M.A. Theoretical insights into the reaction and inhibition mechanism of metal-independent retaining glycosyltransferase responsible for mycothiol biosynthesis |
| topic_facet |
Biosynthesis Electronic structure Enzymes Free energy Biochemical research Concerted reactions Enzymatic reaction Glycosyl transferase Glycosyltransferases Inhibition mechanisms Mycobacterium tuberculosis Reaction mechanism Biochemistry amidase bacterial protein cysteine glycopeptide glycosyltransferase inositol metal mycothiol N-acetyl-1-D-inosityl-2-amino-2-deoxy-alpha-D-glucopyranoside deacetylase antagonists and inhibitors biocatalysis biosynthesis chemistry metabolism Mycobacterium tuberculosis quantum theory Amidohydrolases Bacterial Proteins Biocatalysis Cysteine Glycopeptides Glycosyltransferases Inositol Metals Mycobacterium tuberculosis Quantum Theory |
| description |
Understanding enzymatic reactions with atomic resolution has proven in recent years to be of tremendous interest for biochemical research, and thus, the use of QM/MM methods for the study of reaction mechanisms is experiencing a continuous growth. Glycosyltransferases (GTs) catalyze the formation of glycosidic bonds, and are important for many biotechnological purposes, including drug targeting. Their reaction product may result with only one of the two possible stereochemical outcomes for the reacting anomeric center, and therefore, they are classified as either inverting or retaining GTs. While the inverting GT reaction mechanism has been widely studied, the retaining GT mechanism has always been controversial and several questions remain open to this day. In this work, we take advantage of our recent GPU implementation of a pure QM(DFT-PBE)/MM approach to explore the reaction and inhibition mechanism of MshA, a key retaining GT responsible for the first step of mycothiol biosynthesis, a low weight thiol compound found in pathogens like Mycobacterium tuberculosis that is essential for its survival under oxidative stress conditions. Our results show that the reaction proceeds via a front-side SNi-like concerted reaction mechanism (DNAN in IUPAC nomenclature) and has a 17.5 kcal/mol free energy barrier, which is in remarkable agreement with experimental data. Detailed analysis shows that the key reaction step is the diphosphate leaving group dissociation, leading to an oxocarbenium-ion-like transition state. In contrast, fluorinated substrate analogues increase the reaction barrier significantly, rendering the enzyme effectively inactive. Detailed analysis of the electronic structure along the reaction suggests that this particular inhibition mechanism is associated with fluorine's high electronegative nature, which hinders phosphate release and proper stabilization of the transition state. © 2016 American Chemical Society. |
| format |
JOUR |
| author |
Capurro, J.I.B. Hopkins, C.W. Sottile, G.P. González Lebrero, M.C. Roitberg, A.E. Marti, M.A. |
| author_facet |
Capurro, J.I.B. Hopkins, C.W. Sottile, G.P. González Lebrero, M.C. Roitberg, A.E. Marti, M.A. |
| author_sort |
Capurro, J.I.B. |
| title |
Theoretical insights into the reaction and inhibition mechanism of metal-independent retaining glycosyltransferase responsible for mycothiol biosynthesis |
| title_short |
Theoretical insights into the reaction and inhibition mechanism of metal-independent retaining glycosyltransferase responsible for mycothiol biosynthesis |
| title_full |
Theoretical insights into the reaction and inhibition mechanism of metal-independent retaining glycosyltransferase responsible for mycothiol biosynthesis |
| title_fullStr |
Theoretical insights into the reaction and inhibition mechanism of metal-independent retaining glycosyltransferase responsible for mycothiol biosynthesis |
| title_full_unstemmed |
Theoretical insights into the reaction and inhibition mechanism of metal-independent retaining glycosyltransferase responsible for mycothiol biosynthesis |
| title_sort |
theoretical insights into the reaction and inhibition mechanism of metal-independent retaining glycosyltransferase responsible for mycothiol biosynthesis |
| url |
http://hdl.handle.net/20.500.12110/paper_15206106_v121_n3_p471_Capurro |
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