1KUF

High-resolution Crystal Structure of a Snake Venom Metalloproteinase from Taiwan Habu

Summary for 1KUF

• Entry DOI: 10.2210/pdb1kuf/pdb
• Related: 1KUG
• Descriptor: metalloproteinase, CADMIUM ION (3 entities in total)
• Functional Keywords: alpha/beta protein, hydrolase
• Biological source: Protobothrops mucrosquamatus
• Cellular location: Secreted: O57413
• Total number of polymer chains: 1
• Total formula weight: 24502.92

Authors

Huang, K.F.,Chiou, S.H.,Ko, T.P.,Yuann, J.M.,Wang, A.H.J. (deposition date: 2002-01-21, release date: 2002-07-03, Last modification date: 2024-11-06)

Primary citation

Huang, K.F.,Chiou, S.H.,Ko, T.P.,Yuann, J.M.,Wang, A.H.
The 1.35 A structure of cadmium-substituted TM-3, a snake-venom metalloproteinase from Taiwan habu: elucidation of a TNFalpha-converting enzyme-like active-site structure with a distorted octahedral geometry of cadmium.
Acta Crystallogr.,Sect.D, 58:1118-1128, 2002

PubMed Abstract: The crystal structure of TM-3, a small snake-venom metalloproteinase (SVMP) isolated from Taiwan habu (Trimeresurus mucrosquamatus), was determined at 1.35 A resolution with resultant R and R(free) values of 0.181 and 0.204, respectively. The overall structure of TM-3 is an oblate ellipsoid that contains three disulfide crosslinks, Cys118-Cys197, Cys159-Cys181 and Cys161-Cys164. It exhibits the typical structural features of SVMPs and is closely related to the structure of the catalytic proteinase domain of TNFalpha-converting enzyme (TACE). In the present structure, the essential catalytic zinc ion was found to be replaced by a cadmium ion during crystallization, as revealed by atomic absorption analysis and X-ray data. This cadmium ion is bound to six ligands, including three conserved histidines and three water molecules, displaying the coordination geometry of a distorted octahedron. One of the water molecules is proposed to play the role of stabilizing the tetrahedral intermediate during the catalysis of SVMPs. The putative S'(1) specificity pocket of TM-3 is relatively shallow, in contrast to the deep pockets of adamalysin II, atrolysin C and H(2)-proteinase, but is similar to those in acutolysin A and TACE. The shallow pocket is a consequence of the presence of the non-conserved disulfide bond Cys159-Cys181 and the residue Gln174 at the bottom of the S'(1) pocket. The results indicate that the active-site structure of TM-3, among the know structures of SVMPs examined thus far, is most similar to that of TACE owing to their close disulfide configurations and the S'(1) specificity pocket.

PubMed: 12077431
DOI: 10.1107/S090744490200656X

Experimental method

X-RAY DIFFRACTION (1.35 Å)