PDBsum entry 5amm

Oxidoreductase

PDB id: 5amm

Contents

Protein chains

267 a.a.

Ligands

HEM ×2

Metals

_CA ×2

__K ×2

Waters ×95

References listed in PDB file

Key reference

• Title: &Quot;bind and crawl" association mechanism of leishmania major peroxidase and cytochrome c revealed by brownian and molecular dynamics simulations.
• Authors: J.B.Fields, S.A.Hollingsworth, G.Chreifi, M.Heyden, A.P.Arce, H.I.Magaña-Garcia, T.L.Poulos, D.J.Tobias.
• Ref.: Biochemistry, 2015, 54, 7272-7282. [DOI no: 10.1021/acs.biochem.5b00569]
• PubMed id: 26598276

Abstract

Leishmania major, the parasitic causative agent of leishmaniasis, produces a heme peroxidase (LmP), which catalyzes the peroxidation of mitochondrial cytochrome c (LmCytc) for protection from reactive oxygen species produced by the host. The association of LmP and LmCytc, which is known from kinetics measurements to be very fast (∼10(8) M(-1) s(-1)), does not involve major conformational changes and has been suggested to be dominated by electrostatic interactions. We used Brownian dynamics simulations to investigate the mechanism of formation of the LmP-LmCytc complex. Our simulations confirm the importance of electrostatic interactions involving the negatively charged D211 residue at the LmP active site, and reveal a previously unrecognized role in complex formation for negatively charged residues in helix A of LmP. The crystal structure of the D211N mutant of LmP reported herein is essentially identical to that of wild-type LmP, reinforcing the notion that it is the loss of charge at the active site, and not a change in structure, that reduces the association rate of the D211N variant of LmP. The Brownian dynamics simulations further show that complex formation occurs via a "bind and crawl" mechanism, in which LmCytc first docks to a location on helix A that is far from the active site, forming an initial encounter complex, and then moves along helix A to the active site. An atomistic molecular dynamics simulation confirms the helix A binding site, and steady state activity assays and stopped-flow kinetics measurements confirm the role of helix A charges in the association mechanism.