This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.
Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.
1brg
From Proteopedia
(Difference between revisions)
| (2 intermediate revisions not shown.) | |||
| Line 1: | Line 1: | ||
==CRYSTALLOGRAPHIC ANALYSIS OF PHE->LEU SUBSTITUTION IN THE HYDROPHOBIC CORE OF BARNASE== | ==CRYSTALLOGRAPHIC ANALYSIS OF PHE->LEU SUBSTITUTION IN THE HYDROPHOBIC CORE OF BARNASE== | ||
| - | <StructureSection load='1brg' size='340' side='right' caption='[[1brg]], [[Resolution|resolution]] 2.20Å' scene=''> | + | <StructureSection load='1brg' size='340' side='right'caption='[[1brg]], [[Resolution|resolution]] 2.20Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>[[1brg]] is a 3 chain structure with sequence from [ | + | <table><tr><td colspan='2'>[[1brg]] is a 3 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=1BRG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1BRG FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2Å</td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</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=1brg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1brg OCA], [https://pdbe.org/1brg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1brg RCSB], [https://www.ebi.ac.uk/pdbsum/1brg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1brg 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. |
== 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/br/1brg_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/br/1brg_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> | ||
| Line 19: | Line 20: | ||
</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=1brg 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=1brg ConSurf]. | ||
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
| - | <div style="background-color:#fffaf0;"> | ||
| - | == Publication Abstract from PubMed == | ||
| - | The crystal structure of a barnase mutant, Phe-->Leu7 has been determined to 2.2 A resolution. No structural rearrangement is observed near the mutated residue. The F7L mutation is highly destabilizing and this is caused by the loss of extensive van der Waals contacts that wild-type Phe7 made with its neighbouring residues, and the exposure of a large hydrophobic pocket on the surface of the protein. The side-chain conformations of the mutated Leu7 residue have torsion angles chi(1) ranging from -138 degrees to -168 degrees and chi(2) ranging from +16 degrees to +70 degrees, for the three molecules in the asymmetric unit. These angles do not agree with the most frequently observed conformations in the protein side-chain rotamer library [Ponder & Richards (1987). J. Mol. Biol. 193, 775-791]. However, when compared to a more recent 'backbone-dependent' rotamer library [Dunbrack & Karplus (1993). J. Mol. Biol. 230, 543-574], the side-chain conformation of Leu7 agrees well with that of the most frequently observed rotamers. The side-chain conformation of Leu7 was found to be dictated by two factors: it has the lowest conformational energy and it buries the most hydrophobic surface area. | ||
| - | |||
| - | Crystallographic analysis of Phe-->Leu substitution in the hydrophobic core of barnase.,Chen YW, Fersht AR, Henrick K Acta Crystallogr D Biol Crystallogr. 1995 Mar 1;51(Pt 2):220-31. PMID:15299323<ref>PMID:15299323</ref> | ||
| - | |||
| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| - | </div> | ||
| - | <div class="pdbe-citations 1brg" style="background-color:#fffaf0;"></div> | ||
==See Also== | ==See Also== | ||
| - | *[[ | + | *[[Barnase 3D structures|Barnase 3D structures]] |
| - | + | *[[Ribonuclease 3D structures|Ribonuclease 3D structures]] | |
| - | + | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| - | [[Category: | + | [[Category: Bacillus amyloliquefaciens]] |
| - | [[Category: | + | [[Category: Large Structures]] |
| - | [[Category: | + | [[Category: Chen YW]] |
| - | [[Category: | + | [[Category: Fersht AR]] |
| + | [[Category: Henrick K]] | ||
Current revision
CRYSTALLOGRAPHIC ANALYSIS OF PHE->LEU SUBSTITUTION IN THE HYDROPHOBIC CORE OF BARNASE
| |||||||||||

