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Title: Sulfur K-Edge XAS Studies of the Effect of DNA Binding on the [Fe 4 S 4 ] Site in EndoIII and MutY

Abstract

S K-edge X-ray absorption spectroscopy (XAS) was used to study the [Fe4S4] clusters in the DNA repair glycosylases EndoIII and MutY to evaluate the effects of DNA binding and solvation on Fe–S bond covalencies (i.e., the amount of S 3p character mixed into the Fe 3d valence orbitals). Increased covalencies in both iron–thiolate and iron–sulfide bonds would stabilize the oxidized state of the [Fe4S4] clusters. Our results are compared to those on previously studied [Fe4S4] model complexes, ferredoxin (Fd), and to new data on high-potential iron–sulfur protein (HiPIP). A limited decrease in covalency is observed upon removal of solvent water from EndoIII and MutY, opposite to the significant increase observed for Fd, where the [Fe4S4] cluster is solvent exposed. Importantly, in EndoIII and MutY, a large increase in covalency is observed upon DNA binding, which is due to the effect of its negative charge on the iron–sulfur bonds. Furthermore, in EndoIII, this change in covalency can be quantified and makes a significant contribution to the observed decrease in reduction potential found experimentally in DNA repair proteins, enabling their HiPIP-like redox behavior.

Authors:
 [1];  [2];  [3];  [2];  [2]; ORCiD logo [3]; ORCiD logo [2];  [4];  [1]; ORCiD logo [1]
+ Show Author Affiliations
  1. Stanford Univ., CA (United States). Dept. of Chemistry; SLAC National Accelerator Lab., Menlo Park, CA (United States). Stanford Synchrotron Radiation Lightsource
  2. California Inst. of Technology (CalTech), Pasadena, CA (United States). Division of Chemistry
  3. Univ. of California, Davis, CA (United States). Dept. of Chemistry
  4. SLAC National Accelerator Lab., Menlo Park, CA (United States). Stanford Synchrotron Radiation Lightsource
Publication Date:
Research Org.:
SLAC National Accelerator Lab., Menlo Park, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER); National Institutes of Health (NIH)
OSTI Identifier:
1394069
Grant/Contract Number:  
AC02-76SF00515; CA069875; F31 AG040954; GM040392; GM103393; GM120087
Resource Type:
Accepted Manuscript
Journal Name:
Journal of the American Chemical Society
Additional Journal Information:
Journal Volume: 139; Journal Issue: 33; Journal ID: ISSN 0002-7863
Publisher:
American Chemical Society (ACS)
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY

Citation Formats

Ha, Yang, Arnold, Anna R., Nuñez, Nicole N., Bartels, Phillip L., Zhou, Andy, David, Sheila S., Barton, Jacqueline K., Hedman, Britt, Hodgson, Keith O., and Solomon, Edward I. Sulfur K-Edge XAS Studies of the Effect of DNA Binding on the [Fe 4 S 4 ] Site in EndoIII and MutY. United States: N. p., 2017. Web. doi:10.1021/jacs.7b03966.
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Ha, Yang, Arnold, Anna R., Nuñez, Nicole N., Bartels, Phillip L., Zhou, Andy, David, Sheila S., Barton, Jacqueline K., Hedman, Britt, Hodgson, Keith O., & Solomon, Edward I. Sulfur K-Edge XAS Studies of the Effect of DNA Binding on the [Fe 4 S 4 ] Site in EndoIII and MutY. United States. https://doi.org/10.1021/jacs.7b03966
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Ha, Yang, Arnold, Anna R., Nuñez, Nicole N., Bartels, Phillip L., Zhou, Andy, David, Sheila S., Barton, Jacqueline K., Hedman, Britt, Hodgson, Keith O., and Solomon, Edward I. Tue . "Sulfur K-Edge XAS Studies of the Effect of DNA Binding on the [Fe 4 S 4 ] Site in EndoIII and MutY". United States. https://doi.org/10.1021/jacs.7b03966. https://www.osti.gov/servlets/purl/1394069.
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@article{osti_1394069,
title = {Sulfur K-Edge XAS Studies of the Effect of DNA Binding on the [Fe 4 S 4 ] Site in EndoIII and MutY},
author = {Ha, Yang and Arnold, Anna R. and Nuñez, Nicole N. and Bartels, Phillip L. and Zhou, Andy and David, Sheila S. and Barton, Jacqueline K. and Hedman, Britt and Hodgson, Keith O. and Solomon, Edward I.},
abstractNote = {S K-edge X-ray absorption spectroscopy (XAS) was used to study the [Fe4S4] clusters in the DNA repair glycosylases EndoIII and MutY to evaluate the effects of DNA binding and solvation on Fe–S bond covalencies (i.e., the amount of S 3p character mixed into the Fe 3d valence orbitals). Increased covalencies in both iron–thiolate and iron–sulfide bonds would stabilize the oxidized state of the [Fe4S4] clusters. Our results are compared to those on previously studied [Fe4S4] model complexes, ferredoxin (Fd), and to new data on high-potential iron–sulfur protein (HiPIP). A limited decrease in covalency is observed upon removal of solvent water from EndoIII and MutY, opposite to the significant increase observed for Fd, where the [Fe4S4] cluster is solvent exposed. Importantly, in EndoIII and MutY, a large increase in covalency is observed upon DNA binding, which is due to the effect of its negative charge on the iron–sulfur bonds. Furthermore, in EndoIII, this change in covalency can be quantified and makes a significant contribution to the observed decrease in reduction potential found experimentally in DNA repair proteins, enabling their HiPIP-like redox behavior.},
doi = {10.1021/jacs.7b03966},
journal = {Journal of the American Chemical Society},
number = 33,
volume = 139,
place = {United States},
year = {Tue Jul 18 00:00:00 EDT 2017},
month = {Tue Jul 18 00:00:00 EDT 2017}
}
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https://doi.org/10.1021/jacs.7b03966
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    Works referencing / citing this record:

    A combined Far-FTIR, FTIR Spectromicroscopy, and DFT Study of the Effect of DNA Binding on the [4Fe4S] Cluster Site in EndoIII
    journal, February 2020

    Direct experimental evaluation of ligand-induced backbonding in nickel metallacyclic complexes
    journal, January 2019

    VMD: Visual molecular dynamics
    journal, February 1996

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