Cargando…

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...

Descripción completa

Detalles Bibliográficos
Autores principales: 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
Formato: Online Artículo Texto
Lenguaje:English
Publicado: American Association for the Advancement of Science 2021
Materias:
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
_version_ 1783630540395511808
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
work_keys_str_mv AT rosesamuell anunprecedentedinsightintothecatalyticmechanismofcoppernitritereductasefromatomicresolutionanddamagefreestructures
AT antonyuksvetlanav anunprecedentedinsightintothecatalyticmechanismofcoppernitritereductasefromatomicresolutionanddamagefreestructures
AT sasakidaisuke anunprecedentedinsightintothecatalyticmechanismofcoppernitritereductasefromatomicresolutionanddamagefreestructures
AT yamashitakeitaro anunprecedentedinsightintothecatalyticmechanismofcoppernitritereductasefromatomicresolutionanddamagefreestructures
AT hiratakunio anunprecedentedinsightintothecatalyticmechanismofcoppernitritereductasefromatomicresolutionanddamagefreestructures
AT uenogo anunprecedentedinsightintothecatalyticmechanismofcoppernitritereductasefromatomicresolutionanddamagefreestructures
AT agohideo anunprecedentedinsightintothecatalyticmechanismofcoppernitritereductasefromatomicresolutionanddamagefreestructures
AT eadyrobertr anunprecedentedinsightintothecatalyticmechanismofcoppernitritereductasefromatomicresolutionanddamagefreestructures
AT toshatakehiko anunprecedentedinsightintothecatalyticmechanismofcoppernitritereductasefromatomicresolutionanddamagefreestructures
AT yamamotomasaki anunprecedentedinsightintothecatalyticmechanismofcoppernitritereductasefromatomicresolutionanddamagefreestructures
AT hasnainssamar anunprecedentedinsightintothecatalyticmechanismofcoppernitritereductasefromatomicresolutionanddamagefreestructures
AT rosesamuell unprecedentedinsightintothecatalyticmechanismofcoppernitritereductasefromatomicresolutionanddamagefreestructures
AT antonyuksvetlanav unprecedentedinsightintothecatalyticmechanismofcoppernitritereductasefromatomicresolutionanddamagefreestructures
AT sasakidaisuke unprecedentedinsightintothecatalyticmechanismofcoppernitritereductasefromatomicresolutionanddamagefreestructures
AT yamashitakeitaro unprecedentedinsightintothecatalyticmechanismofcoppernitritereductasefromatomicresolutionanddamagefreestructures
AT hiratakunio unprecedentedinsightintothecatalyticmechanismofcoppernitritereductasefromatomicresolutionanddamagefreestructures
AT uenogo unprecedentedinsightintothecatalyticmechanismofcoppernitritereductasefromatomicresolutionanddamagefreestructures
AT agohideo unprecedentedinsightintothecatalyticmechanismofcoppernitritereductasefromatomicresolutionanddamagefreestructures
AT eadyrobertr unprecedentedinsightintothecatalyticmechanismofcoppernitritereductasefromatomicresolutionanddamagefreestructures
AT toshatakehiko unprecedentedinsightintothecatalyticmechanismofcoppernitritereductasefromatomicresolutionanddamagefreestructures
AT yamamotomasaki unprecedentedinsightintothecatalyticmechanismofcoppernitritereductasefromatomicresolutionanddamagefreestructures
AT hasnainssamar unprecedentedinsightintothecatalyticmechanismofcoppernitritereductasefromatomicresolutionanddamagefreestructures