title: 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.
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.
authors.affiliation: Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.
authors.forename: Kai-Fa
authors.initials: KF
authors.lastname: Huang
authors.forename: Shyh-Horng
authors.initials: SH
authors.lastname: Chiou
authors.forename: Tzu-Ping
authors.initials: TP
authors.lastname: Ko
authors.forename: Jeu-Ming
authors.initials: JM
authors.lastname: Yuann
authors.forename: Andrew H-J
authors.initials: AH
authors.lastname: Wang
mesh_terms: D051722:ADAM Proteins; D000072198:ADAM17 Protein; D000595:Amino Acid Sequence; D000818:Animals; D001665:Binding Sites; D002104:Cadmium / Q000737:chemistry*; D017364:Collagenases / Q000737:chemistry; D003435:Crotalid Venoms / Q000737:chemistry*; D018360:Crystallography, X-Ray / Q000379:methods*; D004220:Disulfides; D004583:Electrons; D005973:Glutamine / Q000737:chemistry; D006639:Histidine / Q000737:chemistry; D008024:Ligands; D008666:Metalloendopeptidases / Q000737:chemistry*; D008958:Models, Molecular; D015233:Models, Statistical; D008969:Molecular Sequence Data; D011485:Protein Binding; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D017386:Sequence Homology, Amino Acid; D012910:Snake Venoms / Q000737:chemistry*; D014409:Tumor Necrosis Factor-alpha / Q000737:chemistry*; D017819:Viperidae
chemical_list: D003435:Crotalid Venoms; D004220:Disulfides; D008024:Ligands; D012910:Snake Venoms; D014409:Tumor Necrosis Factor-alpha; D002104:Cadmium; D005973:Glutamine; D006639:Histidine; D051722:ADAM Proteins; D017364:Collagenases; D008666:Metalloendopeptidases; C470841:TM-3 protein, Trimeresurus mucrosquamatus; C115407:acutolysin A; C071288:astacin; D000072198:ADAM17 Protein