NDLI: Protein Dynamics Control the Progression and Efficiency of the Catalytic Reaction Cycle of the Escherichia coli DNA-Repair Enzyme AlkB

Content Provider	Journal of Biological Chemistry (JBC)
Author	Ergel, Burçe Gill, Michelle L. Brown, Lewis Yu, Bomina Iii, Arthur G. Palmer Hunt, John F. Palmer, Arthur G.
Abstract	A central goal of enzymology is to understand the physicochemical mechanisms that enable proteins to catalyze complex chemical reactions with high efficiency. Recent methodological advances enable the contribution of protein dynamics to enzyme efficiency to be explored more deeply. Here, we utilize enzymological and biophysical studies, including NMR measurements of conformational dynamics, to develop a quantitative mechanistic scheme for the DNA repair enzyme AlkB. Like other iron/2-oxoglutarate-dependent dioxygenases, AlkB employs a two-step mechanism in which oxidation of 2-oxoglutarate generates a highly reactive enzyme-bound oxyferryl intermediate that, in the case of AlkB, slowly hydroxylates an alkylated nucleobase. Our results demonstrate that a microsecond-to-millisecond time scale conformational transition facilitates the proper sequential order of substrate binding to AlkB. Mutations altering the dynamics of this transition allow generation of the oxyferryl intermediate but promote its premature quenching by solvent, which uncouples 2-oxoglutarate turnover from nucleobase oxidation. Therefore, efficient catalysis by AlkB depends upon the dynamics of a specific conformational transition, establishing another paradigm for the control of enzyme function by protein dynamics.
Related Links	http://www.jbc.org/content/289/43/29584.abstract
Ending Page	29601
Starting Page	29584
Page Count	18
File Format	HTM / HTML PDF
ISSN	00219258
Journal	Journal of Biological Chemistry (JBC)
Issue Number	43
Volume Number	289
DOI	10.1074/jbc.M114.575647
e-ISSN	1083351X
Language	English
Publisher	American Society for Biochemistry and Molecular Biology
Publisher Date	2014-10-24
Access Restriction	Open
Subject Keyword	DNA Repair Enzyme Mechanism Nuclear Magnetic Resonance (NMR) Protein Dynamic X-ray Crystallography AlkB Fe-2OG Dioxygenase Catalytic Efficiency Fluorescence Spectroscopy Molecular Biophysics
Content Type	Text
Resource Type	Article
Subject	Cell Biology Biochemistry Molecular Biology

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Protein Dynamics Control the Progression and Efficiency of the Catalytic Reaction Cycle of the Escherichia coli DNA-Repair Enzyme AlkB*

Protein dynamics control the progression and efficiency of the catalytic reaction cycle of the Escherichia coli DNA-repair enzyme AlkB.

Resonance Assignments of Escherichia Coli AlkB: A Key 2-oxoglutarate and Fe(II) Dependent Dioxygenase of the Adaptive DNA-repair Response

AlkB Dioxygenase Preferentially Repairs Protonated Substrates SPECIFICITY AGAINST EXOCYCLIC ADDUCTS AND MOLECULAR MECHANISM OF ACTION

Minimal Methylated Substrate and Extended Substrate Range of Escherichia coli AlkB Protein, a 1-Methyladenine-DNA Dioxygenase

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Interaction with Single-stranded DNA-binding Protein Stimulates Escherichia coli Ribonuclease HI Enzymatic Activity

Protein Dynamics Control the Progression and Efficiency of the Catalytic Reaction Cycle of the Escherichia coli DNA-Repair Enzyme AlkB

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Protein Dynamics Control the Progression and Efficiency of the Catalytic Reaction Cycle of the Escherichia coli DNA-Repair Enzyme AlkB*

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