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Title: Neutron and Atomic Resolution X-ray Structures of a Lytic Polysaccharide Monooxygenase Reveal Copper-Mediated Dioxygen Binding and Evidence for N-Terminal Deprotonation

A 1.1 Å resolution, room-temperature X-ray structure and a 2.1 Å resolution neutron structure of a chitin-degrading lytic polysaccharide monooxygenase domain from the bacterium Jonesia denitrificans (JdLPMO10A) show a putative dioxygen species equatorially bound to the active site copper. We found that both structures show an elongated density for the dioxygen, most consistent with a Cu(II)-bound peroxide. The coordination environment is consistent with Cu(II). Furthermore, in the neutron and X-ray structures, difference maps reveal the N-terminal amino group, involved in copper coordination, is present as a mixed ND 2 and ND , suggesting a role for the copper ion in shifting the pK a of the amino terminus.
Authors:
 [1] ;  [2] ;  [2] ; ORCiD logo [3] ;  [2] ;  [2] ;  [4] ;  [3] ; ORCiD logo [3] ;  [1] ; ORCiD logo [1]
  1. Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
  2. Norwegian Univ., of Life Sciences (NMBU), As (Norway). Faculty of Chemistry, Biotechnology and Food Science
  3. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Biology and Soft Matter Division
  4. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Advanced Light Source (ALS)
Publication Date:
Report Number(s):
LA-UR-16-29648
Journal ID: ISSN 0006-2960; 101148
Grant/Contract Number:
AC05-00OR22725; AC02-05CH11231; AC52-06NA25396
Type:
Accepted Manuscript
Journal Name:
Biochemistry
Additional Journal Information:
Journal Volume: 56; Journal Issue: 20; Journal ID: ISSN 0006-2960
Publisher:
American Chemical Society (ACS)
Research Org:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
Sponsoring Org:
USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22). Scientific User Facilities Division
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; Biological Science; biofuel neutron crystallography structure protein enzyme
OSTI Identifier:
1376613
Alternate Identifier(s):
OSTI ID: 1407879; OSTI ID: 1472029

Bacik, John-Paul, Mekasha, Sophanit, Forsberg, Zarah, Kovalevsky, Andrey Y., Vaaje-Kolstad, Gustav, Eijsink, Vincent G. H., Nix, Jay C., Coates, Leighton, Cuneo, Matthew J., Unkefer, Clifford J., and Chen, Julian C. -H.. Neutron and Atomic Resolution X-ray Structures of a Lytic Polysaccharide Monooxygenase Reveal Copper-Mediated Dioxygen Binding and Evidence for N-Terminal Deprotonation. United States: N. p., Web. doi:10.1021/acs.biochem.7b00019.
Bacik, John-Paul, Mekasha, Sophanit, Forsberg, Zarah, Kovalevsky, Andrey Y., Vaaje-Kolstad, Gustav, Eijsink, Vincent G. H., Nix, Jay C., Coates, Leighton, Cuneo, Matthew J., Unkefer, Clifford J., & Chen, Julian C. -H.. Neutron and Atomic Resolution X-ray Structures of a Lytic Polysaccharide Monooxygenase Reveal Copper-Mediated Dioxygen Binding and Evidence for N-Terminal Deprotonation. United States. doi:10.1021/acs.biochem.7b00019.
Bacik, John-Paul, Mekasha, Sophanit, Forsberg, Zarah, Kovalevsky, Andrey Y., Vaaje-Kolstad, Gustav, Eijsink, Vincent G. H., Nix, Jay C., Coates, Leighton, Cuneo, Matthew J., Unkefer, Clifford J., and Chen, Julian C. -H.. 2017. "Neutron and Atomic Resolution X-ray Structures of a Lytic Polysaccharide Monooxygenase Reveal Copper-Mediated Dioxygen Binding and Evidence for N-Terminal Deprotonation". United States. doi:10.1021/acs.biochem.7b00019. https://www.osti.gov/servlets/purl/1376613.
@article{osti_1376613,
title = {Neutron and Atomic Resolution X-ray Structures of a Lytic Polysaccharide Monooxygenase Reveal Copper-Mediated Dioxygen Binding and Evidence for N-Terminal Deprotonation},
author = {Bacik, John-Paul and Mekasha, Sophanit and Forsberg, Zarah and Kovalevsky, Andrey Y. and Vaaje-Kolstad, Gustav and Eijsink, Vincent G. H. and Nix, Jay C. and Coates, Leighton and Cuneo, Matthew J. and Unkefer, Clifford J. and Chen, Julian C. -H.},
abstractNote = {A 1.1 Å resolution, room-temperature X-ray structure and a 2.1 Å resolution neutron structure of a chitin-degrading lytic polysaccharide monooxygenase domain from the bacterium Jonesia denitrificans (JdLPMO10A) show a putative dioxygen species equatorially bound to the active site copper. We found that both structures show an elongated density for the dioxygen, most consistent with a Cu(II)-bound peroxide. The coordination environment is consistent with Cu(II). Furthermore, in the neutron and X-ray structures, difference maps reveal the N-terminal amino group, involved in copper coordination, is present as a mixed ND2 and ND–, suggesting a role for the copper ion in shifting the pKa of the amino terminus.},
doi = {10.1021/acs.biochem.7b00019},
journal = {Biochemistry},
number = 20,
volume = 56,
place = {United States},
year = {2017},
month = {5}
}