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An unprecedented insight into the catalytic mechanism of copper nitrite reductase from atomic-resolution and damage-free structures
Copper-containing nitrite reductases (CuNiRs), encoded by nirK gene, are found in all kingdoms of life with only 5% of CuNiR denitrifiers having two or more copies of nirK. Recently, we have identified two copies of nirK genes in several α-proteobacteria of the order Rhizobiales including Bradyrhizo...
Autores principales: | , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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American Association for the Advancement of Science
2021
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7775769/ https://www.ncbi.nlm.nih.gov/pubmed/33523860 http://dx.doi.org/10.1126/sciadv.abd8523 |
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author | Rose, Samuel L. Antonyuk, Svetlana V. Sasaki, Daisuke Yamashita, Keitaro Hirata, Kunio Ueno, Go Ago, Hideo Eady, Robert R. Tosha, Takehiko Yamamoto, Masaki Hasnain, S. Samar |
author_facet | Rose, Samuel L. Antonyuk, Svetlana V. Sasaki, Daisuke Yamashita, Keitaro Hirata, Kunio Ueno, Go Ago, Hideo Eady, Robert R. Tosha, Takehiko Yamamoto, Masaki Hasnain, S. Samar |
author_sort | Rose, Samuel L. |
collection | PubMed |
description | Copper-containing nitrite reductases (CuNiRs), encoded by nirK gene, are found in all kingdoms of life with only 5% of CuNiR denitrifiers having two or more copies of nirK. Recently, we have identified two copies of nirK genes in several α-proteobacteria of the order Rhizobiales including Bradyrhizobium sp. ORS 375, encoding a four-domain heme-CuNiR and the usual two-domain CuNiR (Br(2D)NiR). Compared with two of the best-studied two-domain CuNiRs represented by the blue (AxNiR) and green (AcNiR) subclasses, Br(2D)NiR, a blue CuNiR, shows a substantially lower catalytic efficiency despite a sequence identity of ~70%. Advanced synchrotron radiation and x-ray free-electron laser are used to obtain the most accurate (atomic resolution with unrestrained SHELX refinement) and damage-free (free from radiation-induced chemistry) structures, in as-isolated, substrate-bound, and product-bound states. This combination has shed light on the protonation states of essential catalytic residues, additional reaction intermediates, and how catalytic efficiency is modulated. |
format | Online Article Text |
id | pubmed-7775769 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | American Association for the Advancement of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-77757692021-01-14 An unprecedented insight into the catalytic mechanism of copper nitrite reductase from atomic-resolution and damage-free structures Rose, Samuel L. Antonyuk, Svetlana V. Sasaki, Daisuke Yamashita, Keitaro Hirata, Kunio Ueno, Go Ago, Hideo Eady, Robert R. Tosha, Takehiko Yamamoto, Masaki Hasnain, S. Samar Sci Adv Research Articles Copper-containing nitrite reductases (CuNiRs), encoded by nirK gene, are found in all kingdoms of life with only 5% of CuNiR denitrifiers having two or more copies of nirK. Recently, we have identified two copies of nirK genes in several α-proteobacteria of the order Rhizobiales including Bradyrhizobium sp. ORS 375, encoding a four-domain heme-CuNiR and the usual two-domain CuNiR (Br(2D)NiR). Compared with two of the best-studied two-domain CuNiRs represented by the blue (AxNiR) and green (AcNiR) subclasses, Br(2D)NiR, a blue CuNiR, shows a substantially lower catalytic efficiency despite a sequence identity of ~70%. Advanced synchrotron radiation and x-ray free-electron laser are used to obtain the most accurate (atomic resolution with unrestrained SHELX refinement) and damage-free (free from radiation-induced chemistry) structures, in as-isolated, substrate-bound, and product-bound states. This combination has shed light on the protonation states of essential catalytic residues, additional reaction intermediates, and how catalytic efficiency is modulated. American Association for the Advancement of Science 2021-01-01 /pmc/articles/PMC7775769/ /pubmed/33523860 http://dx.doi.org/10.1126/sciadv.abd8523 Text en Copyright © 2021 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution License 4.0 (CC BY). https://creativecommons.org/licenses/by/4.0/ https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution license (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Articles Rose, Samuel L. Antonyuk, Svetlana V. Sasaki, Daisuke Yamashita, Keitaro Hirata, Kunio Ueno, Go Ago, Hideo Eady, Robert R. Tosha, Takehiko Yamamoto, Masaki Hasnain, S. Samar An unprecedented insight into the catalytic mechanism of copper nitrite reductase from atomic-resolution and damage-free structures |
title | An unprecedented insight into the catalytic mechanism of copper nitrite reductase from atomic-resolution and damage-free structures |
title_full | An unprecedented insight into the catalytic mechanism of copper nitrite reductase from atomic-resolution and damage-free structures |
title_fullStr | An unprecedented insight into the catalytic mechanism of copper nitrite reductase from atomic-resolution and damage-free structures |
title_full_unstemmed | An unprecedented insight into the catalytic mechanism of copper nitrite reductase from atomic-resolution and damage-free structures |
title_short | An unprecedented insight into the catalytic mechanism of copper nitrite reductase from atomic-resolution and damage-free structures |
title_sort | unprecedented insight into the catalytic mechanism of copper nitrite reductase from atomic-resolution and damage-free structures |
topic | Research Articles |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7775769/ https://www.ncbi.nlm.nih.gov/pubmed/33523860 http://dx.doi.org/10.1126/sciadv.abd8523 |
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