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Title: Structural insights into the mechanism of oxidative activation of heme-free H-NOX from Vibrio cholerae

Abstract

Bacterial heme nitric oxide/oxygen (H-NOX) domains are nitric oxide (NO) or oxygen sensors. This activity is mediated through binding of the ligand to a heme cofactor. However, H-NOX from Vibrio cholerae (Vc H-NOX) can be easily purified in a heme-free state that is capable of reversibly responding to oxidation, suggesting a heme-independent function as a redox sensor. This occurs by oxidation of Cys residues at a zinc-binding site conserved in a subset of H-NOX homologs. Remarkably, zinc is not lost from the protein upon oxidation, although its ligation environment is significantly altered. Using a combination of computational and experimental approaches, we have characterized localized structural changes that accompany the formation of specific disulfide bonds between Cys residues upon oxidation. Furthermore, the larger-scale structural changes accompanying oxidation appear to mimic those changes observed upon NO binding to the heme-bound form. Thus, Vc H-NOX and its homologs may act as both redox and NO sensors by completely separate mechanisms.

Authors:
 [1];  [2];  [3];  [1]; ORCiD logo [1]
  1. New Mexico State Univ., Las Cruces, NM (United States). Dept. of Chemistry and Biochemistry
  2. Reed College, Portland, OR (United States). Dept. of Chemistry
  3. New Mexico State Univ., Las Cruces, NM (United States). Dept. of Plant and Environmental Sciences
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)
OSTI Identifier:
1624989
Grant/Contract Number:  
AC02-76SF00515
Resource Type:
Accepted Manuscript
Journal Name:
Biochemical Journal
Additional Journal Information:
Journal Volume: 477; Journal Issue: 6; Journal ID: ISSN 0264-6021
Publisher:
Biochemical Society
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; Biochemistry & Molecular Biology; disulphide bonds; redox signalling; zinc; Computational Biology; Molecular Bases of Health & Disease; Signaling

Citation Formats

Mukhopadhyay, Roma, Chacón, Kelly N., Jarvis, Jacqueline M., Talipov, Marat R., and Yukl, Erik T.. Structural insights into the mechanism of oxidative activation of heme-free H-NOX from Vibrio cholerae. United States: N. p., 2020. Web. https://doi.org/10.1042/bcj20200124.
Mukhopadhyay, Roma, Chacón, Kelly N., Jarvis, Jacqueline M., Talipov, Marat R., & Yukl, Erik T.. Structural insights into the mechanism of oxidative activation of heme-free H-NOX from Vibrio cholerae. United States. https://doi.org/10.1042/bcj20200124
Mukhopadhyay, Roma, Chacón, Kelly N., Jarvis, Jacqueline M., Talipov, Marat R., and Yukl, Erik T.. Mon . "Structural insights into the mechanism of oxidative activation of heme-free H-NOX from Vibrio cholerae". United States. https://doi.org/10.1042/bcj20200124. https://www.osti.gov/servlets/purl/1624989.
@article{osti_1624989,
title = {Structural insights into the mechanism of oxidative activation of heme-free H-NOX from Vibrio cholerae},
author = {Mukhopadhyay, Roma and Chacón, Kelly N. and Jarvis, Jacqueline M. and Talipov, Marat R. and Yukl, Erik T.},
abstractNote = {Bacterial heme nitric oxide/oxygen (H-NOX) domains are nitric oxide (NO) or oxygen sensors. This activity is mediated through binding of the ligand to a heme cofactor. However, H-NOX from Vibrio cholerae (Vc H-NOX) can be easily purified in a heme-free state that is capable of reversibly responding to oxidation, suggesting a heme-independent function as a redox sensor. This occurs by oxidation of Cys residues at a zinc-binding site conserved in a subset of H-NOX homologs. Remarkably, zinc is not lost from the protein upon oxidation, although its ligation environment is significantly altered. Using a combination of computational and experimental approaches, we have characterized localized structural changes that accompany the formation of specific disulfide bonds between Cys residues upon oxidation. Furthermore, the larger-scale structural changes accompanying oxidation appear to mimic those changes observed upon NO binding to the heme-bound form. Thus, Vc H-NOX and its homologs may act as both redox and NO sensors by completely separate mechanisms.},
doi = {10.1042/bcj20200124},
journal = {Biochemical Journal},
number = 6,
volume = 477,
place = {United States},
year = {2020},
month = {3}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record

Figures / Tables:

Figure 1 Figure 1: Conservation of zinc binding sites among H-NOX homologues. (A) Sequence similarity network including 599 sequences filtered such that only edges associated with E-values less than 10−47 are included in the network. Sequences are represented by rectangles colored according to class. (B) Multiple sequence alignment of three representative sequencesmore » from each group in (A). Putative zinc-binding residues are highlighted in yellow. Species names are abbreviated as follows: (Group 1) Calg, Cellulophaga algiola; Rsli, Runella slithyformis; Mext, Methylobacterium extorquans; (Group 2) Vcho, Vibrio cholerae; Sone, Shewanella oneidensis; Lpne, Legionella pneumophila; (Group 3) Msp, Mycobacterium sp.; Cvib, Caulobacter vibrioides; Psp, Pseudomonas sp. DY-1; (Group 4) Vhar, Vibrio harveyi; Vnig, Vibrio nigripulchritudo; Psan, Photobacterium sanguinicancri. (C) Zinc coordination environment in a Vc H-NOX homology model. Each of the residues in the figure has been mutated to Ala and those indicated by asterisks result in insoluble protein.« less

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