7S5O

Crystal structure of Cytochrome c' beta from Nitrosomonas europaea ATCC 19718

Summary for 7S5O

• Entry DOI: 10.2210/pdb7s5o/pdb
• Descriptor: Cytochrome_P460 domain-containing protein, HEME C, SULFATE ION, ... (5 entities in total)
• Functional Keywords: ssgcid, cytochrome_p460 domain-containing protein, nitrosomonas europaea, ne0824, structural genomics, seattle structural genomics center for infectious disease, metal binding protein
• Biological source: Nitrosomonas europaea (strain ATCC 19718 / CIP 103999 / KCTC 2705 / NBRC 14298)
• Total number of polymer chains: 3
• Total formula weight: 59771.91

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID) (deposition date: 2021-09-11, release date: 2022-03-30, Last modification date: 2024-10-23)

Primary citation

Abendroth, J.,Buchko, G.W.,Liew, F.N.,Nguyen, J.N.,Kim, H.J.
Structural Characterization of Cytochrome c ' beta-Met from an Ammonia-Oxidizing Bacterium.
Biochemistry, 61:563-574, 2022

PubMed Abstract: The ammonia-oxidizing bacterium expresses two cytochromes in the P460 superfamily that are predicted to be structurally similar. In one, cytochrome (cyt) P460, the substrate hydroxylamine (NHOH) is converted to nitric oxide (NO) and nitrous oxide (NO) requiring a unique heme-lysyl cross-link in the catalytic cofactor. In the second, cyt , the cross-link is absent, and the cytochrome instead binds HO forming a ferryl species similar to compound II of peroxidases. Here, we report the 1.80 Å crystal structure of cyt ─a well-expressed protein in with a lysine to a methionine replacement at the cross-linking position. The structure of cyt is characterized by a large β-sheet typical of P460 members; however, several localized structural differences render cyt distinct. This includes a large lasso-like loop at the "top" of the cytochrome that is not observed in other structurally characterized members. Active site variation is also observed, especially in comparison to its closest homologue cyt from the methane-oxidizing Bath, which also lacks the cross-link. The phenylalanine "cap" which is presumed to control small ligand access to the distal heme iron is replaced with an arginine, reminiscent of the strictly conserved distal arginine in peroxidases and to the NHOH-oxidizing cytochromes P460. A critical proton-transferring glutamate residue required for NHOH oxidation is nevertheless missing in the active site. This in part explains the inability of cyt to oxidize NHOH. Our structure also rationalizes the absence of a methionyl cross-link, although the side chain's spatial position in the structure does not eliminate the possibility that it could form under certain conditions.

PubMed: 35315646
DOI: 10.1021/acs.biochem.1c00640

Experimental method

X-RAY DIFFRACTION (1.8 Å)