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Title: Binuclear Cu A formation in biosynthetic models of Cu A in azurin proceeds via a novel Cu(Cys) 2His mononuclear copper intermediate

Cu A is a binuclear electron transfer (ET) center found in cytochrome c oxidases (C cOs), nitrous oxide reductases (N 2ORs), and nitric oxide reductase (NOR). In these proteins, the Cu A centers facilitate efficient ET ( k ET > 10 4 s –1) under low thermodynamic driving forces (10–90 mV). While the structure and functional properties of Cu A are well understood, a detailed mechanism of the incorporation of copper into the protein and the identity of the intermediates formed during the Cu A maturation process are still lacking. Previous studies of the Cu A assembly mechanism in vitro using a biosynthetic model Cu A center in azurin (Cu AAz) identified a novel intermediate X (I x) during reconstitution of the binuclear site. However, because of the instability of I x and the coexistence of other Cu centers, such as Cu A' and type 1 copper centers, the identity of this intermediate could not be established. In this paper, we report the mechanism of Cu A assembly using variants of Glu114XCu AAz (X = Gly, Ala, Leu, or Gln), the backbone carbonyl of which acts as a ligand to the Cu A site, with a major focus on characterizationmore » of the novel intermediate I x. We show that Cu A assembly in these variants proceeds through several types of Cu centers, such as mononuclear red type 2 Cu, the novel intermediate I x, and blue type 1 Cu. Our results show that the backbone flexibility of the Glu114 residue is an important factor in determining the rates of T2Cu → I x formation, suggesting that Cu A formation is facilitated by swinging of the ligand loop, which internalizes the T2Cu capture complex to the protein interior. The kinetic data further suggest that the nature of the Glu114 side chain influences the time scales on which these intermediates are formed, the wavelengths of the absorption peaks, and how cleanly one intermediate is converted to another. Through careful understanding of these mechanisms and optimization of the conditions, we have obtained I x in ~80–85% population in these variants, which allowed us to employ ultraviolet–visible, electron paramagnetic resonance, and extended X-ray absorption fine structure spectroscopic techniques to identify the I x as a mononuclear Cu(Cys) 2(His) complex. Finally, because some of the intermediates have been proposed to be involved in the assembly of native Cu A, these results shed light on the structural features of the important intermediates and mechanism of Cu A formation.« less
Authors:
 [1] ;  [1] ;  [2] ;  [1] ;  [1] ;  [1] ;  [1] ;  [2] ;  [1]
  1. Univ. of Illinois at Urbana-Champaign, Urbana, IL (United States)
  2. Oregon Health & Sciences Univ., Portland, OR (United States)
Publication Date:
Grant/Contract Number:
AC02-98CH10886
Type:
Accepted Manuscript
Journal Name:
Biochemistry
Additional Journal Information:
Journal Volume: 54; Journal Issue: 39; Journal ID: ISSN 0006-2960
Publisher:
American Chemical Society (ACS)
Research Org:
Univ. of Illinois at Urbana-Champaign, IL (United States)
Sponsoring Org:
USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22)
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
OSTI Identifier:
1344903

Chakraborty, Saumen, Polen, Michael J., Chacon, Kelly N., Wilson, Tiffany D., Yu, Yang, Reed, Julian, Nilges, Mark J., Blackburn, Ninian J., and Lu, Yi. Binuclear CuA formation in biosynthetic models of CuA in azurin proceeds via a novel Cu(Cys)2His mononuclear copper intermediate. United States: N. p., Web. doi:10.1021/acs.biochem.5b00659.
Chakraborty, Saumen, Polen, Michael J., Chacon, Kelly N., Wilson, Tiffany D., Yu, Yang, Reed, Julian, Nilges, Mark J., Blackburn, Ninian J., & Lu, Yi. Binuclear CuA formation in biosynthetic models of CuA in azurin proceeds via a novel Cu(Cys)2His mononuclear copper intermediate. United States. doi:10.1021/acs.biochem.5b00659.
Chakraborty, Saumen, Polen, Michael J., Chacon, Kelly N., Wilson, Tiffany D., Yu, Yang, Reed, Julian, Nilges, Mark J., Blackburn, Ninian J., and Lu, Yi. 2015. "Binuclear CuA formation in biosynthetic models of CuA in azurin proceeds via a novel Cu(Cys)2His mononuclear copper intermediate". United States. doi:10.1021/acs.biochem.5b00659. https://www.osti.gov/servlets/purl/1344903.
@article{osti_1344903,
title = {Binuclear CuA formation in biosynthetic models of CuA in azurin proceeds via a novel Cu(Cys)2His mononuclear copper intermediate},
author = {Chakraborty, Saumen and Polen, Michael J. and Chacon, Kelly N. and Wilson, Tiffany D. and Yu, Yang and Reed, Julian and Nilges, Mark J. and Blackburn, Ninian J. and Lu, Yi},
abstractNote = {CuA is a binuclear electron transfer (ET) center found in cytochrome c oxidases (CcOs), nitrous oxide reductases (N2ORs), and nitric oxide reductase (NOR). In these proteins, the CuA centers facilitate efficient ET (kET > 104 s–1) under low thermodynamic driving forces (10–90 mV). While the structure and functional properties of CuA are well understood, a detailed mechanism of the incorporation of copper into the protein and the identity of the intermediates formed during the CuA maturation process are still lacking. Previous studies of the CuA assembly mechanism in vitro using a biosynthetic model CuA center in azurin (CuAAz) identified a novel intermediate X (Ix) during reconstitution of the binuclear site. However, because of the instability of Ix and the coexistence of other Cu centers, such as CuA' and type 1 copper centers, the identity of this intermediate could not be established. In this paper, we report the mechanism of CuA assembly using variants of Glu114XCuAAz (X = Gly, Ala, Leu, or Gln), the backbone carbonyl of which acts as a ligand to the CuA site, with a major focus on characterization of the novel intermediate Ix. We show that CuA assembly in these variants proceeds through several types of Cu centers, such as mononuclear red type 2 Cu, the novel intermediate Ix, and blue type 1 Cu. Our results show that the backbone flexibility of the Glu114 residue is an important factor in determining the rates of T2Cu → Ix formation, suggesting that CuA formation is facilitated by swinging of the ligand loop, which internalizes the T2Cu capture complex to the protein interior. The kinetic data further suggest that the nature of the Glu114 side chain influences the time scales on which these intermediates are formed, the wavelengths of the absorption peaks, and how cleanly one intermediate is converted to another. Through careful understanding of these mechanisms and optimization of the conditions, we have obtained Ix in ~80–85% population in these variants, which allowed us to employ ultraviolet–visible, electron paramagnetic resonance, and extended X-ray absorption fine structure spectroscopic techniques to identify the Ix as a mononuclear Cu(Cys)2(His) complex. Finally, because some of the intermediates have been proposed to be involved in the assembly of native CuA, these results shed light on the structural features of the important intermediates and mechanism of CuA formation.},
doi = {10.1021/acs.biochem.5b00659},
journal = {Biochemistry},
number = 39,
volume = 54,
place = {United States},
year = {2015},
month = {9}
}