6E0Y

A131Q mutant of cyt P460 of Nitrosomonas sp. AL212 with bound NH2OH

Summary for 6E0Y

• Entry DOI: 10.2210/pdb6e0y/pdb
• Descriptor: Cytochrome P460, HEME C, HYDROXYAMINE, ... (4 entities in total)
• Functional Keywords: nitrification, ammonia-oxidizing bacteria, metal binding protein
• Biological source: Nitrosomonas sp. AL212
• Total number of polymer chains: 4
• Total formula weight: 78190.44

Authors

Smith, M.,Lancaster, K. (deposition date: 2018-07-07, release date: 2019-02-27, Last modification date: 2023-10-11)

Primary citation

Smith, M.A.,Majer, S.H.,Vilbert, A.C.,Lancaster, K.M.
Controlling a burn: outer-sphere gating of hydroxylamine oxidation by a distal base in cytochrome P460.
Chem Sci, 10:3756-3764, 2019

PubMed Abstract: Ammonia oxidizing bacteria (AOB) use the cytotoxic, energetic molecule hydroxylamine (NHOH) as a source of reducing equivalents for cellular respiration. Despite disproportionation or violent decomposition being typical outcomes of reactions of NHOH with iron, AOB and anammox heme P460 proteins including cytochrome (cyt) P460 and hydroxylamine oxidoreductase (HAO) effect controlled, stepwise oxidation of NHOH to nitric oxide (NO). Curiously, a recently characterized cyt P460 variant from the AOB sp. AL212 is able to form all intermediates of cyt P460 catalysis, but is nevertheless incompetent for NHOH oxidation. We now show site-directed mutagenesis, activity assays, spectroscopy, and structural biology that this lack of activity is attributable to the absence of a critical basic glutamate residue in the distal pocket above the heme P460 cofactor. This substitution is the only distinguishing characteristic of a protein that is otherwise effectively structurally and spectroscopically identical to an active variant. This highlights and reinforces a fundamental principal of metalloenzymology: metallocofactor inner-sphere geometric and electronic structures are in many cases insufficient for imbuing reactivity; a precisely defined outer coordination sphere contributed by the polypeptide matrix can be the key differentiator between a metalloenzyme and an unreactive metalloprotein.

PubMed: 31015919
DOI: 10.1039/c9sc00195f

Experimental method

X-RAY DIFFRACTION (2.257 Å)