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Transition State in DNA Polymerase β Catalysis: Rate-Limiting Chemistry Altered by Base-Pair Configuration
[Image: see text] Kinetics studies of dNTP analogues having pyrophosphate-mimicking β,γ-pCXYp leaving groups with variable X and Y substitution reveal striking differences in the chemical transition-state energy for DNA polymerase β that depend on all aspects of base-pairing configurations, includin...
Autores principales: | , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
American
Chemical Society
2014
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3985788/ https://www.ncbi.nlm.nih.gov/pubmed/24580380 http://dx.doi.org/10.1021/bi500101z |
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author | Oertell, Keriann Chamberlain, Brian T. Wu, Yue Ferri, Elena Kashemirov, Boris A. Beard, William A. Wilson, Samuel H. McKenna, Charles E. Goodman, Myron F. |
author_facet | Oertell, Keriann Chamberlain, Brian T. Wu, Yue Ferri, Elena Kashemirov, Boris A. Beard, William A. Wilson, Samuel H. McKenna, Charles E. Goodman, Myron F. |
author_sort | Oertell, Keriann |
collection | PubMed |
description | [Image: see text] Kinetics studies of dNTP analogues having pyrophosphate-mimicking β,γ-pCXYp leaving groups with variable X and Y substitution reveal striking differences in the chemical transition-state energy for DNA polymerase β that depend on all aspects of base-pairing configurations, including whether the incoming dNTP is a purine or pyrimidine and if base-pairings are right (T•A and G•C) or wrong (T•G and G•T). Brønsted plots of the catalytic rate constant (log(k(pol))) versus pK(a4) for the leaving group exhibit linear free energy relationships (LFERs) with negative slopes ranging from −0.6 to −2.0, consistent with chemical rate-determining transition-states in which the active-site adjusts to charge-stabilization demand during chemistry depending on base-pair configuration. The Brønsted slopes as well as the intercepts differ dramatically and provide the first direct evidence that dNTP base recognition by the enzyme–primer–template complex triggers a conformational change in the catalytic region of the active-site that significantly modifies the rate-determining chemical step. |
format | Online Article Text |
id | pubmed-3985788 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | American
Chemical Society |
record_format | MEDLINE/PubMed |
spelling | pubmed-39857882015-03-03 Transition State in DNA Polymerase β Catalysis: Rate-Limiting Chemistry Altered by Base-Pair Configuration Oertell, Keriann Chamberlain, Brian T. Wu, Yue Ferri, Elena Kashemirov, Boris A. Beard, William A. Wilson, Samuel H. McKenna, Charles E. Goodman, Myron F. Biochemistry [Image: see text] Kinetics studies of dNTP analogues having pyrophosphate-mimicking β,γ-pCXYp leaving groups with variable X and Y substitution reveal striking differences in the chemical transition-state energy for DNA polymerase β that depend on all aspects of base-pairing configurations, including whether the incoming dNTP is a purine or pyrimidine and if base-pairings are right (T•A and G•C) or wrong (T•G and G•T). Brønsted plots of the catalytic rate constant (log(k(pol))) versus pK(a4) for the leaving group exhibit linear free energy relationships (LFERs) with negative slopes ranging from −0.6 to −2.0, consistent with chemical rate-determining transition-states in which the active-site adjusts to charge-stabilization demand during chemistry depending on base-pair configuration. The Brønsted slopes as well as the intercepts differ dramatically and provide the first direct evidence that dNTP base recognition by the enzyme–primer–template complex triggers a conformational change in the catalytic region of the active-site that significantly modifies the rate-determining chemical step. American Chemical Society 2014-03-03 2014-03-25 /pmc/articles/PMC3985788/ /pubmed/24580380 http://dx.doi.org/10.1021/bi500101z Text en Copyright © 2014 American Chemical Society |
spellingShingle | Oertell, Keriann Chamberlain, Brian T. Wu, Yue Ferri, Elena Kashemirov, Boris A. Beard, William A. Wilson, Samuel H. McKenna, Charles E. Goodman, Myron F. Transition State in DNA Polymerase β Catalysis: Rate-Limiting Chemistry Altered by Base-Pair Configuration |
title | Transition State in DNA Polymerase β Catalysis:
Rate-Limiting Chemistry Altered by Base-Pair Configuration |
title_full | Transition State in DNA Polymerase β Catalysis:
Rate-Limiting Chemistry Altered by Base-Pair Configuration |
title_fullStr | Transition State in DNA Polymerase β Catalysis:
Rate-Limiting Chemistry Altered by Base-Pair Configuration |
title_full_unstemmed | Transition State in DNA Polymerase β Catalysis:
Rate-Limiting Chemistry Altered by Base-Pair Configuration |
title_short | Transition State in DNA Polymerase β Catalysis:
Rate-Limiting Chemistry Altered by Base-Pair Configuration |
title_sort | transition state in dna polymerase β catalysis:
rate-limiting chemistry altered by base-pair configuration |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3985788/ https://www.ncbi.nlm.nih.gov/pubmed/24580380 http://dx.doi.org/10.1021/bi500101z |
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