2kf5: Difference between revisions
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==Barnase bound to d(CGAC), low pressure== | |||
<StructureSection load='2kf5' size='340' side='right'caption='[[2kf5]]' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[2kf5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_amyloliquefaciens Bacillus amyloliquefaciens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KF5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2KF5 FirstGlance]. <br> | |||
</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=2kf5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2kf5 OCA], [https://pdbe.org/2kf5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2kf5 RCSB], [https://www.ebi.ac.uk/pdbsum/2kf5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2kf5 ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/RNBR_BACAM RNBR_BACAM] Hydrolyzes phosphodiester bonds in RNA, poly- and oligoribonucleotides resulting in 3'-nucleoside monophosphates via 2',3'-cyclophosphate intermediates. | |||
== Evolutionary Conservation == | |||
[[Image:Consurf_key_small.gif|200px|right]] | |||
Check<jmol> | |||
<jmolCheckbox> | |||
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kf/2kf5_consurf.spt"</scriptWhenChecked> | |||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | |||
<text>to colour the structure by Evolutionary Conservation</text> | |||
</jmolCheckbox> | |||
</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=2kf5 ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
In this work we measured 1H NMR chemical shifts for the ribonuclease barnase at pressures from 3 MPa to 200 MPa, both free and bound to d(CGAC). Shift changes with pressure were used as restraints to determine the change in structure with pressure. Free barnase is compressed by approximately 0.7%. The largest changes are on the ligand-binding face close to Lys-27, which is the recognition site for the cleaved phosphate bond. This part of the protein also contains the buried water molecules. In the presence of d(CGAC), the compressibility is reduced by approximately 70% and the region of structural change is altered: the ligand-binding face is now almost incompressible, whereas changes occur at the opposite face. Because compressibility is proportional to mean square volume fluctuation, we conclude that in free barnase, volume fluctuation is largest close to the active site, but when the inhibitor is bound, the fluctuations become much smaller and are located mainly on the opposite face. The timescale of the fluctuations is nanoseconds to microseconds, consistent with the degree of ordering required for the fluctuations, which are intermediate between rapid uncorrelated side-chain dynamics and slow conformational transitions. The high-pressure technique is therefore useful for characterizing motions on this relatively inaccessible timescale. | |||
Pressure-dependent structure changes in barnase on ligand binding reveal intermediate rate fluctuations.,Wilton DJ, Kitahara R, Akasaka K, Pandya MJ, Williamson MP Biophys J. 2009 Sep 2;97(5):1482-90. PMID:19720037<ref>PMID:19720037</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 2kf5" style="background-color:#fffaf0;"></div> | |||
==See Also== | ==See Also== | ||
*[[Barnase|Barnase]] | *[[Barnase 3D structures|Barnase 3D structures]] | ||
*[[Ribonuclease|Ribonuclease]] | *[[Ribonuclease 3D structures|Ribonuclease 3D structures]] | ||
== References == | |||
== | <references/> | ||
< | __TOC__ | ||
</StructureSection> | |||
[[Category: Bacillus amyloliquefaciens]] | [[Category: Bacillus amyloliquefaciens]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: | [[Category: Williamson MP]] | ||
[[Category: | [[Category: Wilton DJ]] | ||
Latest revision as of 12:47, 9 May 2024
Barnase bound to d(CGAC), low pressureBarnase bound to d(CGAC), low pressure
Structural highlights
FunctionRNBR_BACAM Hydrolyzes phosphodiester bonds in RNA, poly- and oligoribonucleotides resulting in 3'-nucleoside monophosphates via 2',3'-cyclophosphate intermediates. Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedIn this work we measured 1H NMR chemical shifts for the ribonuclease barnase at pressures from 3 MPa to 200 MPa, both free and bound to d(CGAC). Shift changes with pressure were used as restraints to determine the change in structure with pressure. Free barnase is compressed by approximately 0.7%. The largest changes are on the ligand-binding face close to Lys-27, which is the recognition site for the cleaved phosphate bond. This part of the protein also contains the buried water molecules. In the presence of d(CGAC), the compressibility is reduced by approximately 70% and the region of structural change is altered: the ligand-binding face is now almost incompressible, whereas changes occur at the opposite face. Because compressibility is proportional to mean square volume fluctuation, we conclude that in free barnase, volume fluctuation is largest close to the active site, but when the inhibitor is bound, the fluctuations become much smaller and are located mainly on the opposite face. The timescale of the fluctuations is nanoseconds to microseconds, consistent with the degree of ordering required for the fluctuations, which are intermediate between rapid uncorrelated side-chain dynamics and slow conformational transitions. The high-pressure technique is therefore useful for characterizing motions on this relatively inaccessible timescale. Pressure-dependent structure changes in barnase on ligand binding reveal intermediate rate fluctuations.,Wilton DJ, Kitahara R, Akasaka K, Pandya MJ, Williamson MP Biophys J. 2009 Sep 2;97(5):1482-90. PMID:19720037[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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