1rkn: Difference between revisions

From Proteopedia
Jump to navigationJump to search
← Older editNewer edit →
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,332,843 edits
No edit summary
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,332,843 edits
No edit summary
Line 1: Line 1:


==Solution structure of 1-110 fragment of Staphylococcal Nuclease with G88W mutation==
==Solution structure of 1-110 fragment of Staphylococcal Nuclease with G88W mutation==
<StructureSection load='1rkn' size='340' side='right'caption='[[1rkn]], [[NMR_Ensembles_of_Models | 12 NMR models]]' scene=''>
<StructureSection load='1rkn' size='340' side='right'caption='[[1rkn]]' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1rkn]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"micrococcus_aureus"_(rosenbach_1884)_zopf_1885 "micrococcus aureus" (rosenbach 1884) zopf 1885]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RKN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RKN FirstGlance]. <br>
<table><tr><td colspan='2'>[[1rkn]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RKN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RKN FirstGlance]. <br>
</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Micrococcal_nuclease Micrococcal nuclease], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.31.1 3.1.31.1] </span></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</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=1rkn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rkn OCA], [https://pdbe.org/1rkn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rkn RCSB], [https://www.ebi.ac.uk/pdbsum/1rkn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rkn ProSAT]</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=1rkn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rkn OCA], [https://pdbe.org/1rkn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rkn RCSB], [https://www.ebi.ac.uk/pdbsum/1rkn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rkn ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/NUC_STAAU NUC_STAAU]] Enzyme that catalyzes the hydrolysis of both DNA and RNA at the 5' position of the phosphodiester bond.
[https://www.uniprot.org/uniprot/A5A520_STAAU A5A520_STAAU]  
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
Line 19: Line 19:
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1rkn ConSurf].
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1rkn ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Folding stability and cooperativity of the three forms of 1-110 residues fragment of staphylococcal nuclease (SNase110) have been studied by various biophysical and NMR methods. Samples of G-88W- and V-66W-mutant SNase110, namely G-88W110 and V-66W110, in aqueous solution and SNase110 in 2.0 M TMAO are adopted in this study. The unfolding transitions and folded conformations of the three SNase fragments were detected by far- and near-ultraviolet circular dichroism and intrinsic tryptophan fluorescence measurements. The tertiary structures and internal motions of the fragments were determined by NMR spectroscopy. Both G-88W and V-66W single mutations as well as a small organic osmolyte (Trimethylamine N-oxide, TMAO) can fold the fragment into a native-like conformation. However, the tertiary structures of the three fragments exhibit different degrees of folding stability and compactness. G-88W110 adopts a relatively rigid structure representing a most stable native-like beta-subdomain conformation of the three fragments. V-66W110- and TMAO-stabilized SNase110 produce less compact structures having a less stable "beta-barrel" structural region. The different folding status accounts for the different backbone dynamic and urea-unfolding transition features of the three fragments. The G-20I/G-29I-mutant variants of the three fragments have provided the evidence that the folding status is correlated closely to the packing of the beta-strands in the beta-barrel of the fragments. The native-like beta-barrel structural region acts as a nonlocal nucleus for folding the fragment. The tertiary folding of the three fragments is initiated by formation of the local nucleation sites at two beta-turn regions, I-18-D-21 and Y-27-Q-30, and developed by the formation of a nonlocal nucleation site at the beta-barrel region. The formation of beta-barrel and overall structure is concerted, but the level of cooperativity is different for the three 1-110 residues SNase fragments.
Folding stability and cooperativity of the three forms of 1-110 residues fragment of staphylococcal nuclease.,Xie T, Liu D, Feng Y, Shan L, Wang J Biophys J. 2007 Mar 15;92(6):2090-107. Epub 2006 Dec 15. PMID:17172296<ref>PMID:17172296</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1rkn" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Staphylococcal nuclease 3D structures|Staphylococcal nuclease 3D structures]]
*[[Staphylococcal nuclease 3D structures|Staphylococcal nuclease 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Micrococcal nuclease]]
[[Category: Staphylococcus aureus]]
[[Category: Feng, Y G]]
[[Category: Feng YG]]
[[Category: Liu, D S]]
[[Category: Liu DS]]
[[Category: Shan, L]]
[[Category: Shan L]]
[[Category: Wang, J F]]
[[Category: Wang JF]]
[[Category: Ye, K Q]]
[[Category: Ye KQ]]
[[Category: Folding]]
[[Category: G88w110]]
[[Category: Hydrolase]]
[[Category: Staphylococcal nuclease]]
Retrieved from "https://proteopedia.org/1rkn"