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| | ==Barnase high pressure structure== | | ==Barnase high pressure structure== |
| - | <StructureSection load='2kf4' size='340' side='right'caption='[[2kf4]], [[NMR_Ensembles_of_Models | 10 NMR models]]' scene=''> | + | <StructureSection load='2kf4' size='340' side='right'caption='[[2kf4]]' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2kf4]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_amyloliquifaciens"_(sic)_fukumoto_1943 "bacillus amyloliquifaciens" (sic) fukumoto 1943]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KF4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2KF4 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2kf4]] 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=2KF4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2KF4 FirstGlance]. <br> |
| - | </td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1a2p|1a2p]], [[2kf3|2kf3]], [[2kf5|2kf5]], [[2kf6|2kf6]]</div></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=2kf4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2kf4 OCA], [https://pdbe.org/2kf4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2kf4 RCSB], [https://www.ebi.ac.uk/pdbsum/2kf4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2kf4 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=2kf4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2kf4 OCA], [https://pdbe.org/2kf4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2kf4 RCSB], [https://www.ebi.ac.uk/pdbsum/2kf4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2kf4 ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == 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.
| + | [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 == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| | + | [[Category: Bacillus amyloliquefaciens]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Williamson, M P]] | + | [[Category: Williamson MP]] |
| - | [[Category: Wilton, D J]] | + | [[Category: Wilton DJ]] |
| - | [[Category: Barnase]]
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| - | [[Category: Endonuclease]]
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| - | [[Category: Hydrolase]]
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| - | [[Category: Nuclease]]
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| - | [[Category: Pressure]]
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| - | [[Category: Ribonuclease]]
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| - | [[Category: Secreted]]
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| - | [[Category: Signaling protein]]
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| Structural highlights
Function
RNBR_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 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[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Wilton DJ, Kitahara R, Akasaka K, Pandya MJ, Williamson MP. Pressure-dependent structure changes in barnase on ligand binding reveal intermediate rate fluctuations. Biophys J. 2009 Sep 2;97(5):1482-90. PMID:19720037 doi:10.1016/j.bpj.2009.06.022
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