2za4: Difference between revisions
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==Crystal Structural Analysis of Barnase-barstar Complex== | ==Crystal Structural Analysis of Barnase-barstar Complex== | ||
<StructureSection load='2za4' size='340' side='right' caption='[[2za4]], [[Resolution|resolution]] 1.58Å' scene=''> | <StructureSection load='2za4' size='340' side='right'caption='[[2za4]], [[Resolution|resolution]] 1.58Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[2za4]] is a 4 chain structure with sequence from [ | <table><tr><td colspan='2'>[[2za4]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_amyloliquefaciens Bacillus amyloliquefaciens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZA4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZA4 FirstGlance]. <br> | ||
</td></tr><tr><td class="sblockLbl"><b>[[ | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.58Å</td></tr> | ||
<tr><td class="sblockLbl"><b>[[ | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr> | ||
<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2za4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2za4 OCA], [https://pdbe.org/2za4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2za4 RCSB], [https://www.ebi.ac.uk/pdbsum/2za4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2za4 ProSAT]</span></td></tr> | ||
<table> | </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 == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
Check<jmol> | Check<jmol> | ||
<jmolCheckbox> | <jmolCheckbox> | ||
<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/za/2za4_consurf.spt"</scriptWhenChecked> | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/za/2za4_consurf.spt"</scriptWhenChecked> | ||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | ||
<text>to colour the structure by Evolutionary Conservation</text> | <text>to colour the structure by Evolutionary Conservation</text> | ||
</jmolCheckbox> | </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/ | </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=2za4 ConSurf]. | ||
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
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From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
</div> | </div> | ||
<div class="pdbe-citations 2za4" style="background-color:#fffaf0;"></div> | |||
==See Also== | ==See Also== | ||
*[[Barnase|Barnase]] | *[[Barnase 3D structures|Barnase 3D structures]] | ||
*[[Barstar|Barstar]] | *[[Barstar 3D structures|Barstar 3D structures]] | ||
*[[Ribonuclease|Ribonuclease]] | *[[Ribonuclease 3D structures|Ribonuclease 3D structures]] | ||
== References == | == References == | ||
<references/> | <references/> | ||
| Line 35: | Line 39: | ||
</StructureSection> | </StructureSection> | ||
[[Category: Bacillus amyloliquefaciens]] | [[Category: Bacillus amyloliquefaciens]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: | [[Category: Ikura T]] | ||
[[Category: | [[Category: Ito N]] | ||
[[Category: | [[Category: Urakubo Y]] | ||
Latest revision as of 16:27, 1 November 2023
Crystal Structural Analysis of Barnase-barstar ComplexCrystal Structural Analysis of Barnase-barstar Complex
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 PubMedThe complex of barnase (bn) and barstar (bs), which has been widely studied as a model for quantitative analysis of protein-protein interactions, is significantly destabilized by a single mutation, namely, bs Asp39 --> Ala, which corresponds to a change of 7.7 kcal x mol(-1) in the free energy of binding. However, there has been no structural information available to explain such a drastic destabilization. In the present study, we determined the structure of the mutant complex at 1.58 A resolution by X-ray crystallography. The complex was similar to the wild-type complex in terms of overall and interface structures; however, the hydrogen bond network mediated by water molecules at the interface was significantly different. Several water molecules filled the cavity created by the mutation and consequently caused rearrangement of the hydrated water molecules at the interface. The water molecules were redistributed into a channel-like structure that penetrated into the complex. Furthermore, molecular dynamics simulations showed that the mutation increased the mobility of water molecules at the interface. Since such a drastic change in hydration was not observed in other mutant complexes of bn and bs, the significant destabilization of the interaction may be due to this channel-like structure of hydrated water molecules. Crystal structural analysis of protein-protein interactions drastically destabilized by a single mutation.,Urakubo Y, Ikura T, Ito N Protein Sci. 2008 Jun;17(6):1055-65. Epub 2008 Apr 25. PMID:18441234[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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