6y5t: Difference between revisions
No edit summary |
No edit summary |
||
| Line 1: | Line 1: | ||
==Crystal structure of savinase at room temperature== | ==Crystal structure of savinase at room temperature== | ||
<StructureSection load='6y5t' size='340' side='right'caption='[[6y5t]]' scene=''> | <StructureSection load='6y5t' size='340' side='right'caption='[[6y5t]], [[Resolution|resolution]] 1.10Å' 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=6Y5T OCA]. For a <b>guided tour on the structure components</b> use [ | <table><tr><td colspan='2'>[[6y5t]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Lederbergia_lenta Lederbergia lenta]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Y5T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6Y5T FirstGlance]. <br> | ||
</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.1Å</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=NA:SODIUM+ION'>NA</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=6y5t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6y5t OCA], [https://pdbe.org/6y5t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6y5t RCSB], [https://www.ebi.ac.uk/pdbsum/6y5t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6y5t ProSAT]</span></td></tr> | |||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/SUBS_LEDLE SUBS_LEDLE] Subtilisin is an extracellular alkaline serine protease, it catalyzes the hydrolysis of proteins and peptide amides. | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
BACKGROUND: Several examples have emerged of enzymes where slow conformational changes are of key importance for function and where low populated conformations in the resting enzyme resemble the conformations of intermediate states in the catalytic process. Previous work on the subtilisin protease, Savinase, from Bacillus lentus by NMR spectroscopy suggested that this enzyme undergoes slow conformational dynamics around the substrate binding site. However, the functional importance of such dynamics is unknown. METHODS: Here we have probed the conformational heterogeneity in Savinase by following the temperature dependent chemical shift changes. In addition, we have measured changes in the local stability of the enzyme when the inhibitor phenylmethylsulfonyl fluoride is bound using hydrogen-deuterium exchange mass spectrometry (HDX-MS). Finally, we have used X-ray crystallography to compare electron densities collected at cryogenic and ambient temperatures and searched for possible low populated alternative conformations in the crystals. RESULTS: The NMR temperature titration shows that Savinase is most flexible around the active site, but no distinct alternative states could be identified. The HDX shows that modification of Savinase with inhibitor has very little impact on the stability of hydrogen bonds and solvent accessibility of the backbone. The most pronounced structural heterogeneities detected in the diffraction data are limited to alternative side-chain rotamers and a short peptide segment that has an alternative main-chain conformation in the crystal at cryo conditions. Collectively, our data show that there is very little structural heterogeneity in the resting state of Savinase and hence that Savinase does not rely on conformational selection to drive the catalytic process. | |||
Conformational heterogeneity of Savinase from NMR, HDX-MS and X-ray diffraction analysis.,Wu S, Nguyen TTTN, Moroz OV, Turkenburg JP, Nielsen JE, Wilson KS, Rand KD, Teilum K PeerJ. 2020 Jun 26;8:e9408. doi: 10.7717/peerj.9408. eCollection 2020. PMID:32617193<ref>PMID:32617193</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 6y5t" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Subtilisin 3D structures|Subtilisin 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Lederbergia lenta]] | |||
[[Category: Moroz O]] | [[Category: Moroz O]] | ||
[[Category: Nielsen JE]] | [[Category: Nielsen JE]] | ||