5AMM

Structure of Leishmania major peroxidase D211N mutant

Summary for 5AMM

• Entry DOI: 10.2210/pdb5amm/pdb
• Related: 5AL9 5ALA
• Descriptor: ASCORBATE PEROXIDASE, PROTOPORPHYRIN IX CONTAINING FE, POTASSIUM ION, ... (5 entities in total)
• Functional Keywords: oxidoreductase
• Biological source: LEISHMANIA MAJOR
• Total number of polymer chains: 2
• Total formula weight: 62578.81

Authors

Chreifi, G.,Fields, J.B.,Hollingsworth, S.A.,Heyden, M.,Arce, A.P.,Magana-Garcia, H.I.,Poulos, T.L.,Tobias, D.J. (deposition date: 2015-03-11, release date: 2015-12-09, Last modification date: 2024-01-10)

Primary citation

Fields, J.B.,Hollingsworth, S.A.,Chreifi, G.,Heyden, M.,Arce, A.P.,Magana-Garcia, H.I.,Poulos, T.L.,Tobias, D.J.
"Bind and Crawl" Association Mechanism of Leishmania Major Peroxidase and Cytochrome C Revealed by Brownian and Molecular Dynamics Simulations.
Biochemistry, 54:7272-, 2015

PubMed 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.

PubMed: 26598276
DOI: 10.1021/ACS.BIOCHEM.5B00569

Experimental method

X-RAY DIFFRACTION (2.09 Å)