PreprintArticleVersion 1This version is not peer-reviewed
Structural Basis of Activation of Zinc-Dependent Peptidase of the Bacteriophage T5 by Calcium Ions: A Glance at the Ion-Dependent Functioning Proteoforms
Version 1
: Received: 30 July 2024 / Approved: 31 July 2024 / Online: 31 July 2024 (14:23:59 CEST)
How to cite:
Prokhorov, D. A.; Mikoulinskaia, G. V.; Kutyshenko, V. P.; Uversky, V. N. Structural Basis of Activation of Zinc-Dependent Peptidase of the Bacteriophage T5 by Calcium Ions: A Glance at the Ion-Dependent Functioning Proteoforms. Preprints2024, 2024072561. https://doi.org/10.20944/preprints202407.2561.v1
Prokhorov, D. A.; Mikoulinskaia, G. V.; Kutyshenko, V. P.; Uversky, V. N. Structural Basis of Activation of Zinc-Dependent Peptidase of the Bacteriophage T5 by Calcium Ions: A Glance at the Ion-Dependent Functioning Proteoforms. Preprints 2024, 2024072561. https://doi.org/10.20944/preprints202407.2561.v1
Prokhorov, D. A.; Mikoulinskaia, G. V.; Kutyshenko, V. P.; Uversky, V. N. Structural Basis of Activation of Zinc-Dependent Peptidase of the Bacteriophage T5 by Calcium Ions: A Glance at the Ion-Dependent Functioning Proteoforms. Preprints2024, 2024072561. https://doi.org/10.20944/preprints202407.2561.v1
APA Style
Prokhorov, D. A., Mikoulinskaia, G. V., Kutyshenko, V. P., & Uversky, V. N. (2024). Structural Basis of Activation of Zinc-Dependent Peptidase of the Bacteriophage T5 by Calcium Ions: A Glance at the Ion-Dependent Functioning Proteoforms. Preprints. https://doi.org/10.20944/preprints202407.2561.v1
Chicago/Turabian Style
Prokhorov, D. A., Victor P. Kutyshenko and Vladimir N. Uversky. 2024 "Structural Basis of Activation of Zinc-Dependent Peptidase of the Bacteriophage T5 by Calcium Ions: A Glance at the Ion-Dependent Functioning Proteoforms" Preprints. https://doi.org/10.20944/preprints202407.2561.v1
Abstract
Endolysin of bacteriophage T5 (EndoT5) is a Zn2+-dependent and Ca2+-activated L-alanyl-D-glutamate peptidase that hydrolyses peptidoglycans during the destruction of the cell wall of the phage host bacterium Escherichia coli. To elucidate the mechanism of calcium activation, the spatial solution structure of EndoT5 in a complex with two ions - catalytic Zn2+ and regulatory Ca2+ (EndoT5-Zn2+Ca2+, PDB ID: 8P3A) was determined by high-resolution NMR and deposited in the Protein Data Bank. We show that coordination of the Ca2+ ion fix the spatial position of polar amino acid residues D113, N115 and S117. As a result, the intramolecular mobility of extended protein loops (residues 40-70 and 111-132) is significantly reduced compared to the mobility of these loops in the structure of an enzyme containing only a catalytic a Zn2+ ion (EndoT5-Zn2+, PDB ID: 2MXZ). In the stabilized EF-like calcium-binding loop (residues 111-132), the number of van der Waals interactions with amino acid residues of the globular core of the protein increases. The binding of the Ca2+ ion is accompanied by the selection of the functional states of both extended loops of the enzyme (residues 40-70 and 111-132), because of which EndoT5-Zn2+Ca2+ acquires the structural integrity necessary for catalysis. Therefore, the mechanism of activation of L-alanyl-D-glutamate peptidase of bacteriophage T5 by Ca2+ ions involves stabilization of the enzyme molecule in a catalytically active “open” conformation. This work sheds light on the structural grounds of the ion-dependent functional proteoforms of this interesting protein.
Copyright:
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