3WFE

Reduced and cyanide-bound cytochrome c-dependent nitric oxide reductase (cNOR) from Pseudomonas aeruginosa in complex with antibody fragment

Summary for 3WFE

• Entry DOI: 10.2210/pdb3wfe/pdb
• Related: 3O0R 3WFB 3WFC 3WFD
• Descriptor: antibody fab fragment light chain, HEME C, antibody fab fragment heavy chain, ... (11 entities in total)
• Functional Keywords: metal-binding, membrane protein, immune system-oxidoreductase complex, immune system/oxidoreductase
• Biological source: Mus musculus; More
• Cellular location: Cell membrane ; Multi-pass membrane protein : Q59647; Cell membrane; Single-pass membrane protein: Q59646
• Total number of polymer chains: 4
• Total formula weight: 119412.45

Authors

Sato, N.,Ishii, S.,Hino, T.,Sugimoto, H.,Fukumori, Y.,Shiro, Y.,Tosha, T. (deposition date: 2013-07-18, release date: 2014-05-28, Last modification date: 2024-10-30)

Primary citation

Sato, N.,Ishii, S.,Sugimoto, H.,Hino, T.,Fukumori, Y.,Sako, Y.,Shiro, Y.,Tosha, T.
Structures of reduced and ligand-bound nitric oxide reductase provide insights into functional differences in respiratory enzymes.
Proteins, 82:1258-1271, 2014

PubMed Abstract: Nitric oxide reductase (NOR) catalyzes the generation of nitrous oxide (N2O) via the reductive coupling of two nitric oxide (NO) molecules at a heme/non-heme Fe center. We report herein on the structures of the reduced and ligand-bound forms of cytochrome c-dependent NOR (cNOR) from Pseudomonas aeruginosa at a resolution of 2.3-2.7 Å, to elucidate structure-function relationships in NOR, and compare them to those of cytochrome c oxidase (CCO) that is evolutionarily related to NOR. Comprehensive crystallographic refinement of the CO-bound form of cNOR suggested that a total of four atoms can be accommodated at the binuclear center. Consistent with this, binding of bulky acetaldoxime (CH3-CH=N-OH) to the binuclear center of cNOR was confirmed by the structural analysis. Active site reduction and ligand binding in cNOR induced only ∼0.5 Å increase in the heme/non-heme Fe distance, but no significant structural change in the protein. The highly localized structural change is consistent with the lack of proton-pumping activity in cNOR, because redox-coupled conformational changes are thought to be crucial for proton pumping in CCO. It also permits the rapid decomposition of cytotoxic NO in denitrification. In addition, the shorter heme/non-heme Fe distance even in the bulky ligand-bound form of cNOR (∼4.5 Å) than the heme/Cu distance in CCO (∼5 Å) suggests the ability of NOR to maintain two NO molecules within a short distance in the confined space of the active site, thereby facilitating N-N coupling to produce a hyponitrite intermediate for the generation of N2O.

PubMed: 24338896
DOI: 10.1002/prot.24492

Experimental method

X-RAY DIFFRACTION (2.49 Å)