6TFD

Crystal structure of nitrite and NO bound three-domain copper-containing nitrite reductase from Hyphomicrobium denitrificans strain 1NES1

Summary for 6TFD

• Entry DOI: 10.2210/pdb6tfd/pdb
• Descriptor: Copper-containing nitrite reductase, COPPER (II) ION, NITRITE ION, ... (5 entities in total)
• Functional Keywords: copper-containing nitrite reductase, hyphomicrobium denitrificans strain 1nes1, electron transfer, oxidoreductase
• Biological source: Hyphomicrobium denitrificans 1NES1
• Total number of polymer chains: 3
• Total formula weight: 147846.71

Authors

Sasaki, D.,Watanabe, T.F.,Eady, R.R.,Garratt, R.C.,Antonyuk, S.V.,Hasnain, S.S. (deposition date: 2019-11-13, release date: 2020-06-10, Last modification date: 2024-01-24)

Primary citation

Sasaki, D.,Watanabe, T.F.,Eady, R.R.,Garratt, R.C.,Antonyuk, S.V.,Hasnain, S.S.
Structures of substrate- and product-bound forms of a multi-domain copper nitrite reductase shed light on the role of domain tethering in protein complexes.
Iucrj, 7:557-565, 2020

PubMed Abstract: Copper-containing nitrite reductases (CuNiRs) are found in all three kingdoms of life and play a major role in the denitrification branch of the global nitro-gen cycle where nitrate is used in place of di-oxy-gen as an electron acceptor in respiratory energy metabolism. Several C- and N-terminal redox domain tethered CuNiRs have been identified and structurally characterized during the last decade. Our understanding of the role of tethered domains in these new classes of three-domain CuNiRs, where an extra cytochrome or cupredoxin domain is tethered to the catalytic two-domain CuNiRs, has remained limited. This is further compounded by a complete lack of substrate-bound structures for these tethered CuNiRs. There is still no substrate-bound structure for any of the as-isolated wild-type tethered enzymes. Here, structures of nitrite and product-bound states from a nitrite-soaked crystal of the N-terminal cupredoxin-tethered enzyme from the strain 1NES1 ( NiR) are provided. These, together with the as-isolated structure of the same species, provide clear evidence for the role of the N-terminal peptide bearing the conserved His27 in water-mediated anchoring of the substrate at the catalytic T2Cu site. Our data indicate a more complex role of tethering than the intuitive advantage for a partner-protein electron-transfer complex by narrowing the conformational search in such a combined system.

PubMed: 32431838
DOI: 10.1107/S2052252520005230

Experimental method

X-RAY DIFFRACTION (2.25 Å)