1kuf
From Proteopedia
(New page: 200px<br /><applet load="1kuf" size="450" color="white" frame="true" align="right" spinBox="true" caption="1kuf, resolution 1.35Å" /> '''High-resolution Crys...) |
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| - | [[Image:1kuf.gif|left|200px]]<br /><applet load="1kuf" size=" | + | [[Image:1kuf.gif|left|200px]]<br /><applet load="1kuf" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1kuf, resolution 1.35Å" /> | caption="1kuf, resolution 1.35Å" /> | ||
'''High-resolution Crystal Structure of a Snake Venom Metalloproteinase from Taiwan Habu'''<br /> | '''High-resolution Crystal Structure of a Snake Venom Metalloproteinase from Taiwan Habu'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The crystal structure of TM-3, a small snake-venom metalloproteinase | + | 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. |
==About this Structure== | ==About this Structure== | ||
| - | 1KUF is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Protobothrops_mucrosquamatus Protobothrops mucrosquamatus] with CD as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Atrolysin_E Atrolysin E], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.24.44 3.4.24.44] Full crystallographic information is available from [http:// | + | 1KUF is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Protobothrops_mucrosquamatus Protobothrops mucrosquamatus] with <scene name='pdbligand=CD:'>CD</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Atrolysin_E Atrolysin E], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.24.44 3.4.24.44] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KUF OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Protobothrops mucrosquamatus]] | [[Category: Protobothrops mucrosquamatus]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
| - | [[Category: Chiou, S | + | [[Category: Chiou, S H.]] |
| - | [[Category: Huang, K | + | [[Category: Huang, K F.]] |
| - | [[Category: Ko, T | + | [[Category: Ko, T P.]] |
| - | [[Category: Wang, A | + | [[Category: Wang, A H.J.]] |
| - | [[Category: Yuann, J | + | [[Category: Yuann, J M.]] |
[[Category: CD]] | [[Category: CD]] | ||
[[Category: alpha/beta protein]] | [[Category: alpha/beta protein]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:38:00 2008'' |
Revision as of 11:38, 21 February 2008
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High-resolution Crystal Structure of a Snake Venom Metalloproteinase from Taiwan Habu
Overview
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.
About this Structure
1KUF is a Single protein structure of sequence from Protobothrops mucrosquamatus with as ligand. Active as Atrolysin E, with EC number 3.4.24.44 Full crystallographic information is available from OCA.
Reference
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., Huang KF, Chiou SH, Ko TP, Yuann JM, Wang AH, Acta Crystallogr D Biol Crystallogr. 2002 Jul;58(Pt 7):1118-28. Epub 2002, Jun 20. PMID:12077431
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