Determinants of the inhibition of a Taiwan habu venom metalloproteinase by its endogenous inhibitors revealed by X-ray crystallography and synthetic inhibitor analogues.
Venoms from crotalid and viperid snakes contain several peptide inhibitors which regulate the proteolytic activities of their snake-venom metalloproteinases (SVMPs) in a reversible manner under physiological conditions. In this report, we describe the high-resolution crystal structures of a SVMP, TM-3, from Taiwan habu (Trimeresurus mucrosquamatus) cocrystallized with the endogenous inhibitors pyroGlu-Asn-Trp (pENW), pyroGlu-Gln-Trp (pEQW) or pyroGlu-Lys-Trp (pEKW). The binding of inhibitors causes some of the residues around the inhibitor-binding environment of TM-3 to slightly move away from the active-site center, and displaces two metal-coordinated water molecules by the C-terminal carboxylic group of the inhibitors. This binding adopts a retro-manner principally stabilized by four possible hydrogen bonds. The Trp indole ring of the inhibitors is stacked against the imidazole of His143 in the S-1 site of the proteinase. Results from the study of synthetic inhibitor analogues showed the primary specificity of Trp residue of the inhibitors at the P-1 site, corroborating the stacking effect observed in our structures. Furthermore, we have made a detailed comparison of our structures with the binding modes of other inhibitors including batimastat, a hydroxamate inhibitor, and a barbiturate derivative. It suggests a close correlation between the inhibitory activity of an inhibitor and its ability to fill the S-1 pocket of the proteinase. Our work may provide insights into the rational design of small molecules that bind to this class of zinc-metalloproteinases.
Huang
Kai-Fa
KF
Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.
Chiou
Shyh-Horng
SH
Ko
Tzu-Ping
TP
Wang
Andrew H-J
AH
D051722:ADAM Proteins; D000072198:ADAM17 Protein; D000818:Animals; D003435:Crotalid Venoms / Q000201:enzymology*; D018360:Crystallography, X-Ray; D004791:Enzyme Inhibitors / Q000138:chemical synthesis / Q000737:chemistry / Q000494:pharmacology; D006639:Histidine / Q000737:chemistry* / Q000378:metabolism; D020784:Matrix Metalloproteinase 8 / Q000737:chemistry / Q000378:metabolism; D061965:Matrix Metalloproteinase Inhibitors; D008666:Metalloendopeptidases / Q000037:antagonists & inhibitors / Q000737:chemistry* / Q000378:metabolism; D008958:Models, Molecular; D009842:Oligopeptides / Q000138:chemical synthesis / Q000737:chemistry* / Q000494:pharmacology; D011485:Protein Binding; D011487:Protein Conformation; D011761:Pyrrolidonecarboxylic Acid / Q000031:analogs & derivatives; D017841:Trimeresurus; D014364:Tryptophan / Q000737:chemistry* / Q000378:metabolism
D003435:Crotalid Venoms; D004791:Enzyme Inhibitors; D061965:Matrix Metalloproteinase Inhibitors; D009842:Oligopeptides; C114010:pyroglutamyl-asparagyl-tryptophan; C114011:pyroglutamyl-glutaminyl-tryptophan; C114009:pyroglutamyl-lysyl-tryptophan; D006639:Histidine; D014364:Tryptophan; D051722:ADAM Proteins; D008666:Metalloendopeptidases; D020784:Matrix Metalloproteinase 8; C089232:atrolysin C; D000072198:ADAM17 Protein; D011761:Pyrrolidonecarboxylic Acid