1QUA
CRYSTAL STRUCTURE OF ACUTOLYSIN-C, A HEMORRHAGIC TOXIN FROM THE SNAKE VENOM OF AGKISTRODON ACUTUS, AT 2.2 A RESOLUTION
Summary for 1QUA
| Entry DOI | 10.2210/pdb1qua/pdb |
| Descriptor | ACUTOLYSIN-C, ZINC ION (3 entities in total) |
| Functional Keywords | metalloprotease, hemorrhagic toxin, snake venom proteinase, agkistrodon acutus, toxin |
| Biological source | Deinagkistrodon acutus (Chinese moccasin) |
| Cellular location | Secreted : Q9W7S2 |
| Total number of polymer chains | 1 |
| Total formula weight | 21523.01 |
| Authors | |
| Primary citation | Zhu, X.,Teng, M.,Niu, L. Structure of acutolysin-C, a haemorrhagic toxin from the venom of Agkistrodon acutus, providing further evidence for the mechanism of the pH-dependent proteolytic reaction of zinc metalloproteinases. Acta Crystallogr.,Sect.D, 55:1834-1841, 1999 Cited by PubMed Abstract: The structure of acutolysin-C, a haemorrhagic zinc metalloproteinase from the venom of Agkistrodon acutus, has been analyzed and refined at 2.2 A resolution. The space group of the crystal is P2(1)2(1)2(1), with unit-cell dimensions a = 46.84, b = 49.52, c = 95.34 A. One molecule was found in each asymmetric unit. The phasing problem was solved by the molecular-replacement program AMoRe. Crystallographic refinement was performed using X-PLOR, leading to final R and free R factors of 0.176 and 0.272, respectively. The residue sequence of acutolysin-C was determined mainly by electron density. No density was found for the first residue at the N--terminus and the last two residues at the C-terminus, which was also the case for most other P-I class snake-venom metalloproteinases (SVMPs). Acutolysin-C has two highly conserved characteristic sequences His142-Glu143-X-X-His146-X-X-Gly149-X-X-His15 2 and Cys162-Ile163-Met164. The enzyme has three disulfide bridges: Cys117-Cys195, Cys157-Cys179 and Cys159-Cys162. The entire structure shows good agreement with that of other reported P-I class SVMPs and has two subdomains with a cleft in which one catalytic zinc ion is localized. However, the local conformation (especially the disulfide configurations), the coordination of the catalytic water molecules and some residue side chains differ compared with other P-I class SVMPs. The proteolytic activities of SVMPs are sensitive to the pH value. The molecular superpositions around the proteolytic active sites of all the P-I class SVMP crystal structures show that the distances between the zinc ion and its ligands are not correlated with the crystallization pH values, although the contact distances between the catalytic water molecule and the O atoms of the Glu143 carboxylate group in the neutral and weakly alkaline structures are shorter than those in weakly acidic structures, and the closer the crystallization pH value of one enzyme is to its optimal activity pH value, the shorter the contact distances. Overall, all P-I class SVMPs have similar conformations in the active-site cleft. The size of the active site is not correlated with the crystallization pH values or the proteolytic activities. The disulfide bridge Cys117-Cys195 is conserved in all crystal structures of P-I class SVMPs, whereas the conformation and number of disulfide bridges in the C-terminal subdomain differ. Acutolysin-C has no structural calcium ion, which may not affect the proteolytic activity or haemorrhagic activity directly. PubMed: 10531480DOI: 10.1107/S0907444999010306 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.2 Å) |
Structure validation
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