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An unprecedented insight into the catalytic mechanism of copper nitrite reductase from atomic-resolution and damage-free structures.

<div class='caption-title'>T2Cu site in as-isolated Br2DNiR: SRX v SF-ROX structures.</div>
<div class='caption-title'>Rotation of His250 (HisCAT) imidazole in each structure.</div>
<div class='caption-title'>T2Cu site in nitrite-bound Br2DNiR: SRX v SF-ROX structures.</div>
Rose SL, Antonyuk SV, Sasaki D, Yamashita K, Hirata K, Ueno G, Ago H, Eady RR, Tosha T, Yamamoto M, Hasnain SS
OpenAccess logo Sci Adv 7 (2021)
Related entries: 6zar, 6zat, 6zau, 6zav, 6zaw, 6zax

Cited: 11 times
EuropePMC logo PMID: 33523860

Abstract

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 2DNiR). Compared with two of the best-studied two-domain CuNiRs represented by the blue (AxNiR) and green (AcNiR) subclasses, Br 2DNiR, 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.

Articles - 6zas mentioned but not cited (1)

  1. Copper nitrite reductase from Sinorhizobium meliloti 2011: Crystal structure and interaction with the physiological versus a nonmetabolically related cupredoxin-like mediator. Ramírez CS, Tolmie C, Opperman DJ, González PJ, Rivas MG, Brondino CD, Ferroni FM. Protein Sci 30 2310-2323 (2021)


Reviews citing this publication (3)

  1. Metalloprotein catalysis: structural and mechanistic insights into oxidoreductases from neutron protein crystallography. Schröder GC, Meilleur F. Acta Crystallogr D Struct Biol 77 1251-1269 (2021)
  2. Mapping Enzyme Landscapes by Time-Resolved Crystallography with Synchrotron and X-Ray Free Electron Laser Light. Wilson MA. Annu Rev Biophys 51 79-98 (2022)
  3. Serial synchrotron and XFEL crystallography for studies of metalloprotein catalysis. Hough MA, Owen RL. Curr Opin Struct Biol 71 232-238 (2021)

Articles citing this publication (7)



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