5I6M

Crystal Structure of Copper Nitrite Reductase at 100K after 7.59 MGy

Summary for 5I6M

• Entry DOI: 10.2210/pdb5i6m/pdb
• Descriptor: Copper-containing nitrite reductase, COPPER (II) ION, ACETATE ION, ... (7 entities in total)
• Functional Keywords: copper nitrite reductase, reaction mechanism, serial crystallography, oxidoreductase
• Biological source: Achromobacter cycloclastes
• Cellular location: Periplasm: P25006
• Total number of polymer chains: 1
• Total formula weight: 37031.23

Authors

Horrell, S.,Hough, M.A.,Strange, R.W. (deposition date: 2016-02-16, release date: 2016-07-13, Last modification date: 2024-01-10)

Primary citation

Horrell, S.,Antonyuk, S.V.,Eady, R.R.,Hasnain, S.S.,Hough, M.A.,Strange, R.W.
Serial crystallography captures enzyme catalysis in copper nitrite reductase at atomic resolution from one crystal.
Iucrj, 3:271-281, 2016

PubMed Abstract: Relating individual protein crystal structures to an enzyme mechanism remains a major and challenging goal for structural biology. Serial crystallography using multiple crystals has recently been reported in both synchrotron-radiation and X-ray free-electron laser experiments. In this work, serial crystallography was used to obtain multiple structures serially from one crystal (MSOX) to study in crystallo enzyme catalysis. Rapid, shutterless X-ray detector technology on a synchrotron MX beamline was exploited to perform low-dose serial crystallography on a single copper nitrite reductase crystal, which survived long enough for 45 consecutive 100 K X-ray structures to be collected at 1.07-1.62 Å resolution, all sampled from the same crystal volume. This serial crystallography approach revealed the gradual conversion of the substrate bound at the catalytic type 2 Cu centre from nitrite to nitric oxide, following reduction of the type 1 Cu electron-transfer centre by X-ray-generated solvated electrons. Significant, well defined structural rearrangements in the active site are evident in the series as the enzyme moves through its catalytic cycle, namely nitrite reduction, which is a vital step in the global denitrification process. It is proposed that such a serial crystallography approach is widely applicable for studying any redox or electron-driven enzyme reactions from a single protein crystal. It can provide a 'catalytic reaction movie' highlighting the structural changes that occur during enzyme catalysis. The anticipated developments in the automation of data analysis and modelling are likely to allow seamless and near-real-time analysis of such data on-site at some of the powerful synchrotron crystallographic beamlines.

PubMed: 27437114
DOI: 10.1107/S205225251600823X

Experimental method

X-RAY DIFFRACTION (1.09 Å)