5AMM image
Deposition Date 2015-03-11
Release Date 2015-12-09
Last Version Date 2024-01-10
Entry Detail
PDB ID:
5AMM
Keywords:
Title:
Structure of Leishmania major peroxidase D211N mutant
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.09 Å
R-Value Free:
0.24
R-Value Work:
0.18
R-Value Observed:
0.18
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:ASCORBATE PEROXIDASE
Gene (Uniprot):APX
Mutations:YES
Chain IDs:A, B
Chain Length:270
Number of Molecules:2
Biological Source:LEISHMANIA MAJOR
Primary Citation
"Bind and Crawl" Association Mechanism of Leishmania Major Peroxidase and Cytochrome C Revealed by Brownian and Molecular Dynamics Simulations.
Biochemistry 54 7272 ? (2015)
PMID: 26598276 DOI: 10.1021/ACS.BIOCHEM.5B00569

Abstact

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.

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