This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.
Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.
6lzo
From Proteopedia
(Difference between revisions)
| Line 1: | Line 1: | ||
==Thermolysin with 1,10-phenanthroline== | ==Thermolysin with 1,10-phenanthroline== | ||
| - | <StructureSection load='6lzo' size='340' side='right'caption='[[6lzo]]' scene=''> | + | <StructureSection load='6lzo' size='340' side='right'caption='[[6lzo]], [[Resolution|resolution]] 1.80Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LZO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6LZO FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6lzo]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_thermoproteolyticus Bacillus thermoproteolyticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LZO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6LZO FirstGlance]. <br> |
| - | </td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6lzo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6lzo OCA], [https://pdbe.org/6lzo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6lzo RCSB], [https://www.ebi.ac.uk/pdbsum/6lzo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6lzo ProSAT]</span></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8Å</td></tr> |
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=PHN:1,10-PHENANTHROLINE'>PHN</scene></td></tr> | ||
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6lzo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6lzo OCA], [https://pdbe.org/6lzo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6lzo RCSB], [https://www.ebi.ac.uk/pdbsum/6lzo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6lzo ProSAT]</span></td></tr> | ||
</table> | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/THER_BACTH THER_BACTH] Extracellular zinc metalloprotease. | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | Metalloproteases and their inhibitors are important in numerous fundamental biochemical phenomena and medical applications. The heterocyclic organic compound, 1,10-phenanthroline, forms a complex with transition metal ions and is a Zn(2+)-chelating metalloprotease inhibitor; however, the mechanism of 1,10-phenanthroline-based chelation inhibition has not been fully elucidated. This study aimed to understand the structural basis of zinc metalloproteinase inhibition by 1,10-phenanthroline. Herein, the crystal structure of thermolysin was determined in the absence and presence of 1,10-phenanthroline at 1.5 and 1.8 A, respectively. In native thermolysin, Zn(2+) at the active site is tetrahedrally coordinated by His142, His146, Glu166, and water molecule and contains three Ca(2+) ions, which are involved in thermostability. In the crystal structure of 1,10-phenanthroline-treated thermolysin crystal, seven 1,10-phenanthroline molecules were observed on the surface of thermolysin. These molecules are stabilized by pi- pi stacking interactions with aromatic amino acids (Phe63, Tyr66, Tyr110, His216, and Try251) or between the 1,10-phenanthrolines. Moreover, interactions with Ser5 and Arg101 were also observed. In this structure, Zn(2+) at the active site was completely chelated, but no large conformational changes were observed in Zn(2+) coordination with amino acid residues. Ca(2+) at the Ca3 site exposed to the solvent was chelated by 1,10-phenanthroline, resulting in a conformational change in the side chain of Asp56 and Gln61. Based on the surface structure, for 1,10-phenanthroline to chelate a metal, it is important that the metal is exposed on the protein surface and that there is no steric hindrance impairing 1,10-phenanthroline access by the amino acids around the metal. | ||
| + | |||
| + | Structural analysis of metal chelation of the metalloproteinase thermolysin by 1,10-phenanthroline.,Nam KH J Inorg Biochem. 2021 Feb;215:111319. doi: 10.1016/j.jinorgbio.2020.111319. Epub , 2020 Dec 5. PMID:33310458<ref>PMID:33310458</ref> | ||
| + | |||
| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 6lzo" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| + | [[Category: Bacillus thermoproteolyticus]] | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Nam KH]] | [[Category: Nam KH]] | ||
Current revision
Thermolysin with 1,10-phenanthroline
| |||||||||||
