6gsq | pdb_00006gsq

Oxidised copper nitrite reductase from Achromobacter cycloclastes determined by serial femtosecond rotation crystallography

spinqualitylabelsall models 6gsq, resolution 1.50Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 6gsq is a 1 chain structure with sequence from "achromobacter_cycloclastes"_(gray_and_thornton)_bergey_et_al. "achromobacter cycloclastes" (gray and thornton) bergey et al.. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: CU, SO4 Gene: nirK ("Achromobacter cycloclastes" (Gray and Thornton) Bergey et al.) Activity: Nitrite reductase (NO-forming), with EC number 1.7.2.1 Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Publication Abstract from PubMed Copper-containing nitrite reductases (CuNiRs) that convert NO2 (-) to NO via a CuCAT-His-Cys-CuET proton-coupled redox system are of central importance in nitrogen-based energy metabolism. These metalloenzymes, like all redox enzymes, are very susceptible to radiation damage from the intense synchrotron-radiation X-rays that are used to obtain structures at high resolution. Understanding the chemistry that underpins the enzyme mechanisms in these systems requires resolutions of better than 2 A. Here, for the first time, the damage-free structure of the resting state of one of the most studied CuNiRs was obtained by combining X-ray free-electron laser (XFEL) and neutron crystallography. This represents the first direct comparison of neutron and XFEL structural data for any protein. In addition, damage-free structures of the reduced and nitrite-bound forms have been obtained to high resolution from cryogenically maintained crystals by XFEL crystallography. It is demonstrated that AspCAT and HisCAT are deprotonated in the resting state of CuNiRs at pH values close to the optimum for activity. A bridging neutral water (D2O) is positioned with one deuteron directed towards AspCAT O(delta1) and one towards HisCAT N(2). The catalytic T2Cu-ligated water (W1) can clearly be modelled as a neutral D2O molecule as opposed to D3O(+) or OD(-), which have previously been suggested as possible alternatives. The bridging water restricts the movement of the unprotonated AspCAT and is too distant to form a hydrogen bond to the O atom of the bound nitrite that interacts with AspCAT. Upon the binding of NO2 (-) a proton is transferred from the bridging water to the O(delta2) atom of AspCAT, prompting electron transfer from T1Cu to T2Cu and reducing the catalytic redox centre. This triggers the transfer of a proton from AspCAT to the bound nitrite, enabling the reaction to proceed. Catalytically important damage-free structures of a copper nitrite reductase obtained by femtosecond X-ray laser and room-temperature neutron crystallography.,Halsted TP, Yamashita K, Gopalasingam CC, Shenoy RT, Hirata K, Ago H, Ueno G, Blakeley MP, Eady RR, Antonyuk SV, Yamamoto M, Hasnain SS IUCrJ. 2019 Jun 23;6(Pt 4):761-772. doi: 10.1107/S2052252519008285. eCollection, 2019 Jul 1. PMID:31316819 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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