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.
3vhq
From Proteopedia
(Difference between revisions)
m (Protected "3vhq" [edit=sysop:move=sysop]) |
|||
| (5 intermediate revisions not shown.) | |||
| Line 1: | Line 1: | ||
| - | '''Unreleased structure''' | ||
| - | + | ==Crystal structure of the Ca6 site mutant of Pro-SA-subtilisin== | |
| + | <StructureSection load='3vhq' size='340' side='right'caption='[[3vhq]], [[Resolution|resolution]] 2.15Å' scene=''> | ||
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[3vhq]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_kodakaraensis_(strain_kod1) Pyrococcus kodakaraensis (strain kod1)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VHQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VHQ FirstGlance]. <br> | ||
| + | </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></td></tr> | ||
| + | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2e1p|2e1p]], [[2zwo|2zwo]], [[2zwp|2zwp]]</div></td></tr> | ||
| + | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">TK1675 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=69014 Pyrococcus kodakaraensis (strain KOD1)])</td></tr> | ||
| + | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Subtilisin Subtilisin], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.62 3.4.21.62] </span></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=3vhq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vhq OCA], [https://pdbe.org/3vhq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vhq RCSB], [https://www.ebi.ac.uk/pdbsum/3vhq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vhq ProSAT]</span></td></tr> | ||
| + | </table> | ||
| + | == Function == | ||
| + | [[https://www.uniprot.org/uniprot/TKSU_THEKO TKSU_THEKO]] Has a broad substrate specificity with a slight preference to large hydrophobic amino acid residues at the P1 position. | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | Tk-subtilisin, a hyperthermostable subtilisin-like serine protease from Thermococcus kodakarensis, matures from the inactive precursor, Pro-Tk-subtilisin (Pro-TKS), upon autoprocessing and degradation of the propeptide (Tkpro). It contains seven Ca(2+) ions. Four of them (Ca2-Ca5) are responsible for folding of Tk-subtilisin. In this study, to clarify the role of the other three Ca(2+) ions (Ca1, Ca6, and Ca7), we constructed Pro-TKS derivatives lacking the Ca1 ion (Pro-TKS/DeltaCa1), Ca6 ion (Pro-TKS/DeltaCa6), and Ca7 ion (Pro-TKS/DeltaCa7), and their active site mutants (Pro-S324A/DeltaCa1, Pro-S324A/DeltaCa6, and Pro-S324A/DeltaCa7, respectively). Pro-TKS/DeltaCa6 and Pro-TKS/DeltaCa7 fully matured into their active forms upon incubation at 80 degrees C for 30 min as did Pro-TKS. The mature enzymes were as active as Tk-subtilisin at 80 degrees C, indicating that the Ca6 and Ca7 ions are not important for activity. In contrast, Pro-TKS/DeltaCa1 matured poorly at 80 degrees C because of the instability of its mature domain. The enzymatic activity of Tk-subtilisin/DeltaCa1 was determined to be 50% of that of Tk-subtilisin using the refolded protein. This result suggests that the Ca1 ion is required for the maximal activity of Tk-subtilisin. The refolding rates of all Pro-S324A derivatives were comparable to that of Pro-S324A (active site mutant of Pro-TKS), indicating that these Ca(2+) ions are not needed for folding of Tk-subtilisin. The stabilities of Pro-S324A/DeltaCa1 and Pro-S324A/DeltaCa6 were decreased by 26.6 and 11.7 degrees C, respectively, in T(m) compared to that of Pro-S324A. The half-lives of Tk-subtilisin/DeltaCa6 and Tk-subtilisin/DeltaCa7 at 95 degrees C were 8- and 4-fold lower than that of Tk-subtilisin, respectively. These results suggest that the Ca1, Ca6, and Ca7 ions, especially the Ca1 ion, contribute to the hyperthermostabilization of Tk-subtilisin. | ||
| - | + | Requirement of Ca(2+) Ions for the Hyperthermostability of Tk-Subtilisin from Thermococcus kodakarensis.,Uehara R, Takeuchi Y, Tanaka SI, Takano K, Koga Y, Kanaya S Biochemistry. 2012 Jun 19. PMID:22686281<ref>PMID:22686281</ref> | |
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| + | </div> | ||
| + | <div class="pdbe-citations 3vhq" style="background-color:#fffaf0;"></div> | ||
| + | |||
| + | ==See Also== | ||
| + | *[[Subtilisin 3D structures|Subtilisin 3D structures]] | ||
| + | == References == | ||
| + | <references/> | ||
| + | __TOC__ | ||
| + | </StructureSection> | ||
| + | [[Category: Large Structures]] | ||
| + | [[Category: Subtilisin]] | ||
| + | [[Category: Kanaya, S]] | ||
| + | [[Category: Koga, Y]] | ||
| + | [[Category: Matsumura, H]] | ||
| + | [[Category: Takano, K]] | ||
| + | [[Category: Takeuchi, Y]] | ||
| + | [[Category: Tanaka, S]] | ||
| + | [[Category: Uehara, R]] | ||
| + | [[Category: Hydrolase]] | ||
| + | [[Category: Proteolysis]] | ||
Current revision
Crystal structure of the Ca6 site mutant of Pro-SA-subtilisin
| |||||||||||
Categories: Large Structures | Subtilisin | Kanaya, S | Koga, Y | Matsumura, H | Takano, K | Takeuchi, Y | Tanaka, S | Uehara, R | Hydrolase | Proteolysis
