Theoretical study on the mechanism of self-cleavage reaction of the glmS ribozyme
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| 024 | 7 | 0 | |a 10.1007/s00214-015-1667-x |2 doi |
| 035 | |a (NATIONALLICENCE)springer-10.1007/s00214-015-1667-x | ||
| 245 | 0 | 0 | |a Theoretical study on the mechanism of self-cleavage reaction of the glmS ribozyme |h [Elektronische Daten] |c [Xue Dong, Zhiyue Tian, Xin Yang, Ying Xue] |
| 520 | 3 | |a The glmS ribozyme is a unique known natural catalytic RNA that takes advantage of a small molecule coenzyme, glucosamine 6-phosphate (GlcN6P). This cofactor in the glmS ribozyme is a general acid-base catalyst. Moreover, the mechanism of self-cleavage reaction of the glmS ribozyme could be studied further. In the present work, the possible mechanisms were investigated at the M06-2X/6-31+G(d,p) level and solvent effect was considered by SMD continuum models. Single-point calculations at the SMD-M06-2X/6-311+G(2df,2p) level were performed for more precise energy predictions. Two possible pathways were considered, the first pathway (path A) is that the G33 (which is in Bacillus anthracis) is deprotonated and serves as the general base, and the other pathway (path B) is that two water molecules deprotonate O2′ of A-1 as an external base and assist to transfer the proton from the O2′ of A-1 to the amine of GlcN6P. Our results indicate that path B is more favorable than path A in solvent. That is, the mechanism in which O2′ of A-1 is deprotonated by one water molecule and the other water bridges the amine of GlcN6P with the first water to continue the reaction, may reduce the free energy barrier. Moreover, in path B, nucleophilic attack of the O2′ is the rate-determining step with a strong hydrogen bond interaction stabilizing the RNA phosphate backbone. | |
| 540 | |a Springer-Verlag Berlin Heidelberg, 2015 | ||
| 690 | 7 | |a glmS ribozyme |2 nationallicence | |
| 690 | 7 | |a Small molecule coenzyme (GlcN6P) |2 nationallicence | |
| 690 | 7 | |a Catalytic mechanism |2 nationallicence | |
| 690 | 7 | |a The density functional theory |2 nationallicence | |
| 700 | 1 | |a Dong |D Xue |u College of Chemistry, Key Lab of Green Chemistry and Technology in Ministry of Education, Sichuan University, 610064, Chengdu, People's Republic of China |4 aut | |
| 700 | 1 | |a Tian |D Zhiyue |u College of Chemistry, Key Lab of Green Chemistry and Technology in Ministry of Education, Sichuan University, 610064, Chengdu, People's Republic of China |4 aut | |
| 700 | 1 | |a Yang |D Xin |u College of Chemistry, Key Lab of Green Chemistry and Technology in Ministry of Education, Sichuan University, 610064, Chengdu, People's Republic of China |4 aut | |
| 700 | 1 | |a Xue |D Ying |u College of Chemistry, Key Lab of Green Chemistry and Technology in Ministry of Education, Sichuan University, 610064, Chengdu, People's Republic of China |4 aut | |
| 773 | 0 | |t Theoretical Chemistry Accounts |d Springer Berlin Heidelberg |g 134/5(2015-05-01), 1-10 |x 1432-881X |q 134:5<1 |1 2015 |2 134 |o 214 | |
| 856 | 4 | 0 | |u https://doi.org/10.1007/s00214-015-1667-x |q text/html |z Onlinezugriff via DOI |
| 898 | |a BK010053 |b XK010053 |c XK010000 | ||
| 900 | 7 | |a Metadata rights reserved |b Springer special CC-BY-NC licence |2 nationallicence | |
| 908 | |D 1 |a research-article |2 jats | ||
| 949 | |B NATIONALLICENCE |F NATIONALLICENCE |b NL-springer | ||
| 950 | |B NATIONALLICENCE |P 856 |E 40 |u https://doi.org/10.1007/s00214-015-1667-x |q text/html |z Onlinezugriff via DOI | ||
| 950 | |B NATIONALLICENCE |P 700 |E 1- |a Dong |D Xue |u College of Chemistry, Key Lab of Green Chemistry and Technology in Ministry of Education, Sichuan University, 610064, Chengdu, People's Republic of China |4 aut | ||
| 950 | |B NATIONALLICENCE |P 700 |E 1- |a Tian |D Zhiyue |u College of Chemistry, Key Lab of Green Chemistry and Technology in Ministry of Education, Sichuan University, 610064, Chengdu, People's Republic of China |4 aut | ||
| 950 | |B NATIONALLICENCE |P 700 |E 1- |a Yang |D Xin |u College of Chemistry, Key Lab of Green Chemistry and Technology in Ministry of Education, Sichuan University, 610064, Chengdu, People's Republic of China |4 aut | ||
| 950 | |B NATIONALLICENCE |P 700 |E 1- |a Xue |D Ying |u College of Chemistry, Key Lab of Green Chemistry and Technology in Ministry of Education, Sichuan University, 610064, Chengdu, People's Republic of China |4 aut | ||
| 950 | |B NATIONALLICENCE |P 773 |E 0- |t Theoretical Chemistry Accounts |d Springer Berlin Heidelberg |g 134/5(2015-05-01), 1-10 |x 1432-881X |q 134:5<1 |1 2015 |2 134 |o 214 | ||