5LWD

Thermolysin in complex with inhibitor (JC96)

Summary for 5LWD

• Entry DOI: 10.2210/pdb5lwd/pdb
• Descriptor: Thermolysin, ZINC ION, CALCIUM ION, ... (7 entities in total)
• Functional Keywords: hydrolase, metalloprotease, hydrolase inhibitor complex
• Biological source: Bacillus thermoproteolyticus
• Cellular location: Secreted: P00800
• Total number of polymer chains: 1
• Total formula weight: 35475.14

Authors

Krimmer, S.G.,Cramer, J.,Heine, A.,Klebe, G. (deposition date: 2016-09-15, release date: 2016-12-21, Last modification date: 2024-01-17)

Primary citation

Cramer, J.,Krimmer, S.G.,Fridh, V.,Wulsdorf, T.,Karlsson, R.,Heine, A.,Klebe, G.
Elucidating the Origin of Long Residence Time Binding for Inhibitors of the Metalloprotease Thermolysin.
ACS Chem. Biol., 12:225-233, 2017

PubMed Abstract: Kinetic parameters of protein-ligand interactions are progressively acknowledged as valuable information for rational drug discovery. However, a targeted optimization of binding kinetics is not easy to achieve, and further systematic studies are necessary to increase the understanding about molecular mechanisms involved. We determined association and dissociation rate constants for 17 inhibitors of the metalloprotease thermolysin by surface plasmon resonance spectroscopy and correlated kinetic data with high-resolution crystal structures in complex with the protein. From the structure-kinetics relationship, we conclude that the strength of interaction with Asn112 correlates with the rate-limiting step of dissociation. This residue is located at the beginning of a β-strand motif that lines the binding cleft and is commonly believed to align a substrate for catalysis. A reduced mobility of the Asn112 side chain owing to an enhanced engagement in charge-assisted hydrogen bonds prevents the conformational adjustment associated with ligand release and transformation of the enzyme to its open state. This hypothesis is supported by kinetic data of ZFLA, a known pseudopeptidic inhibitor of thermolysin, which blocks the conformational transition of Asn112. Interference with this retrograde induced-fit mechanism results in variation of the residence time of thermolysin inhibitors by a factor of 74 000. The high conservation of this structural motif within the M4 and M13 metalloprotease families underpins the importance of this feature and has significant implications for drug discovery.

PubMed: 27959500
DOI: 10.1021/acschembio.6b00979

Experimental method

X-RAY DIFFRACTION (1.23 Å)