6H08

The crystal structure of engineered cytochrome c peroxidase from Saccharomyces cerevisiae with a His175Me-His proximal ligand substitution

Summary for 6H08

• Entry DOI: 10.2210/pdb6h08/pdb
• Descriptor: Cytochrome c peroxidase, mitochondrial, PROTOPORPHYRIN IX CONTAINING FE, COBALT (II) ION, ... (6 entities in total)
• Functional Keywords: engineered cytochrome c peroxidase, saccharomyces cerevisiae, me-his, proximal ligand, oxidoreductase
• Biological source: Saccharomyces cerevisiae (Baker's yeast)
• Total number of polymer chains: 3
• Total formula weight: 104645.41

Authors

Ortmayer, M.,Levy, C.,Green, A.P. (deposition date: 2018-07-06, release date: 2020-02-12, Last modification date: 2020-07-08)

Primary citation

Ortmayer, M.,Fisher, K.,Basran, J.,Wolde-Michael, E.M.,Heyes, D.J.,Levy, C.,Lovelock, S.L.,Anderson, J.L.R.,Raven, E.L.,Hay, S.,Rigby, S.E.J.,Green, A.P.
Rewiring the "Push-Pull" Catalytic Machinery of a Heme Enzyme Using an Expanded Genetic Code.
Acs Catalysis, 10:2735-2746, 2020

PubMed Abstract: Nature employs a limited number of genetically encoded axial ligands to control diverse heme enzyme activities. Deciphering the functional significance of these ligands requires a quantitative understanding of how their electron-donating capabilities modulate the structures and reactivities of the iconic ferryl intermediates compounds I and II. However, probing these relationships experimentally has proven to be challenging as ligand substitutions accessible via conventional mutagenesis do not allow fine tuning of electron donation and typically abolish catalytic function. Here, we exploit engineered translation components to replace the histidine ligand of cytochrome peroxidase (CP) by a less electron-donating -methyl histidine (Me-His) with little effect on the enzyme structure. The rate of formation ( ) and the reactivity ( ) of compound I are unaffected by ligand substitution. In contrast, proton-coupled electron transfer to compound II ( ) is 10-fold slower in CP Me-His, providing a direct link between electron donation and compound II reactivity, which can be explained by weaker electron donation from the Me-His ligand ("the push") affording an electron-deficient ferryl oxygen with reduced proton affinity ("the pull"). The deleterious effects of the Me-His ligand can be fully compensated by introducing a W51F mutation designed to increase "the pull" by removing a hydrogen bond to the ferryl oxygen. Analogous substitutions in ascorbate peroxidase lead to similar activity trends to those observed in CP, suggesting that a common mechanistic strategy is employed by enzymes using distinct electron transfer pathways. Our study highlights how noncanonical active site substitutions can be used to directly probe and deconstruct highly evolved bioinorganic mechanisms.

PubMed: 32550044
DOI: 10.1021/acscatal.9b05129

Experimental method

X-RAY DIFFRACTION (1.9 Å)