1brg: Difference between revisions

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New page: left|200px<br /><applet load="1brg" size="450" color="white" frame="true" align="right" spinBox="true" caption="1brg, resolution 2.2Å" /> '''CRYSTALLOGRAPHIC ANAL...
 
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[[Image:1brg.gif|left|200px]]<br /><applet load="1brg" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1brg, resolution 2.2&Aring;" />
'''CRYSTALLOGRAPHIC ANALYSIS OF PHE->LEU SUBSTITUTION IN THE HYDROPHOBIC CORE OF BARNASE'''<br />


==Overview==
==CRYSTALLOGRAPHIC ANALYSIS OF PHE->LEU SUBSTITUTION IN THE HYDROPHOBIC CORE OF BARNASE==
The crystal structures of two barnase mutants, Tyr78--&gt;Phe and, Ser91--&gt;Ala, have been determined to 2.2 A resolution. In both cases, a, buried hydroxyl group that makes two hydrogen bonds within the protein was, replaced by a hydrogen atom. It is found that neither mutation causes any, structural changes, within the limits of error, compared with wild-type, and so are confirmed to be non-disruptive. Solvent molecules are not, observed in the cavities created by removal of the respective hydroxyl, groups and no new interactions are introduced. The local water structure, surrounding both sites of mutation is well conserved and resembles that of, the wild-type. All four water molecules making contacts with the, side-chain of residue 78 and two water molecules nearest to residue 91 in, the wild-type are found within a sphere of 0.5 A radius, at the equivalent, positions of the respective mutant. No new water molecules are found bound, to any of the hydrogen bond donor or acceptor residues involved in these, two mutation sites. Previous protein engineering experiments established, that the solvent-inaccessible phenolic OH of Tyr78 that makes hydrogen, bonds with two uncharged groups (main-chain NH and CO) contributes 1.4, kcal mol-1 to protein stability, while the solvent-inaccessible OH of, Ser91 that makes hydrogen bonds with an uncharged main-chain NH and a, charged group (O gamma 1) contributes 1.9 kcal mol-1. These stability, measurements can now be attributed primarily to the loss of the hydrogen, bonding interactions because both mutations neither disrupt the respective, protein and local solvent structures, upset the overall hydrogen bonding, pattern nor introduce new interactions. The mutations Tyr78--&gt;Phe and, Ser91--&gt;Ala are thus good examples of "non-disruptive deletions" and the, results of mutagenesis can be analysed at the simplest level.
<StructureSection load='1brg' size='340' side='right'caption='[[1brg]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
== Structural highlights ==
<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='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2&#8491;</td></tr>
<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>
== 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/br/1brg_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=1brg ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
1BRG is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_amyloliquefaciens Bacillus amyloliquefaciens] with ZN as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1BRG OCA].
*[[Barnase 3D structures|Barnase 3D structures]]
 
*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
==Reference==
__TOC__
Contribution of buried hydrogen bonds to protein stability. The crystal structures of two barnase mutants., Chen YW, Fersht AR, Henrick K, J Mol Biol. 1993 Dec 20;234(4):1158-70. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8263918 8263918]
</StructureSection>
[[Category: Bacillus amyloliquefaciens]]
[[Category: Bacillus amyloliquefaciens]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Chen, Y.W.]]
[[Category: Chen YW]]
[[Category: Fersht, A.R.]]
[[Category: Fersht AR]]
[[Category: Henrick, K.]]
[[Category: Henrick K]]
[[Category: ZN]]
[[Category: endonuclease]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 11:51:28 2007''

Latest revision as of 09:38, 7 February 2024

CRYSTALLOGRAPHIC ANALYSIS OF PHE->LEU SUBSTITUTION IN THE HYDROPHOBIC CORE OF BARNASECRYSTALLOGRAPHIC ANALYSIS OF PHE->LEU SUBSTITUTION IN THE HYDROPHOBIC CORE OF BARNASE

Structural highlights

1brg is a 3 chain structure with sequence from Bacillus amyloliquefaciens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.2Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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.

See Also

1brg, resolution 2.20Å

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