Conformational Plasticity and Structure/Function Relationships in Cytochromes P450

Abstract

The cytochrome P450s are a superfamily of enzymes that are found in all kingdoms of living organisms, and typically catalyze the oxidative addition of atomic oxygen to an unactivated C-C or C-H bond. Over 8000 nonredundant sequences of putative and confirmed P450 enzymes have been identified, but three-dimensional structures have been determined for only a small fraction of these. While all P450 enzymes for which structures have been determined share a common global fold, the flexibility and modularity of structure around the active site account for the ability of P450 enzymes to accommodate a vast number of structurally dissimilar substrates and support a wide range of selective oxidations. In this review, known P450 structures are compared, and some structural criteria for prediction of substrate selectivity and reaction type are suggested. The importance of dynamic processes such as redox-dependent and effector-induced conformational changes in determining catalytic competence and regio-and stereoselectivity is discussed, and noncrystallographic methods for characterizing P450 structures and dynamics, in particular, mass spectrometry and nuclear magnetic resonance spectroscopy are reviewed. Antioxid. Redox Signal. 13, 1273-1296.

The Role of Protein-Protein and Protein-Membrane Interactions on P450 Function

“…The CYP1A1 substitution at amino acids 108 to 205 did not seem to alter the relative distribution into ordered and disordered domains; however, when amino acids 206-302 of CYP1A1 were substituted, a higher proportion of the P450 localized to disordered domains, suggesting this region also contributes to the domain selectivity of these enzymes. This region of the protein contains the F and G helices and F-G loop, which interact with the membrane, are involved in substrate binding from the membrane and constitute part of the ceiling of the P450 active site above the heme group (Williams et al, 2003;Yano et al, 2004;Pochapsky et al, 2010;Johnson et al, 2014). Our data show that both the hydrophobic N-terminal sequence and the F-G helices region confer the ordered microdomain selectivity of CYP1A enzymes.…”

Human Cytochrome P450 17A1 Conformational Selection

“…Other biophysical approaches (36 -38) support conformational heterogeneity but must be interpreted within the context of current static structures or that of molecular dynamics simulations whose predictions about molecular motions are not easily verifiable. Although NMR studies for soluble bacterial systems (20,39) and the smaller and more NMR-amenable b 5 protein (32,40) have begun to demonstrate the potential for NMR to provide a high resolution perspective on P450 conformation(s) free of crystallization constraints, protein NMR is a new approach to investigating membrane P450 conformational heterogeneity.…”

“…Like most P450 enzymes, the long protein-spanning I helix of CYP17A1 has a noncanonical hydrogen bonding arrangement just as it passes over the heme. In existing structures of some P450 enzymes (14,23,39), this results in an I helix that has been observed in either a straight conformation or with a kink arising at the midpoint, allowing movement of the N-terminal half of the I helix. In CYP17A1, the carbonyl of Ala-302 clearly hydrogen-bonds to the side chain hydroxyl of Thr-306 rather than the Thr-306 backbone.…”

Substrate and Reaction Specificity of Mycobacterium tuberculosis Cytochrome P450 CYP121

“…In the case of 3, the iron is too far from the site of hydroxylation for such a reaction, and this may explain the low efficiency. It was suggested recently that cis-trans isomerization of the Val 78 -Pro 79 peptide bond in CYP121 could trigger repositioning of the substrate, bringing it close to the heme iron (38). If so, it is clear that this mechanism is not sufficient to allow hydroxylation of 3.…”