1ac8: Difference between revisions
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==VARIATION IN THE STRENGTH OF A CH TO O HYDROGEN BOND IN AN ARTIFICIAL PROTEIN CAVITY (3,4,5-TRIMETHYLTHIAZOLE)== | ==VARIATION IN THE STRENGTH OF A CH TO O HYDROGEN BOND IN AN ARTIFICIAL PROTEIN CAVITY (3,4,5-TRIMETHYLTHIAZOLE)== | ||
<StructureSection load='1ac8' size='340' side='right' caption='[[1ac8]], [[Resolution|resolution]] 2.10Å' scene=''> | <StructureSection load='1ac8' size='340' side='right'caption='[[1ac8]], [[Resolution|resolution]] 2.10Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[1ac8]] is a 1 chain structure with sequence from [ | <table><tr><td colspan='2'>[[1ac8]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AC8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1AC8 FirstGlance]. <br> | ||
</td></tr><tr id=' | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1Å</td></tr> | ||
<tr id=' | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=TMZ:3,4,5-TRIMETHYL-1,3-THIAZOLE'>TMZ</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=1ac8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ac8 OCA], [https://pdbe.org/1ac8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ac8 RCSB], [https://www.ebi.ac.uk/pdbsum/1ac8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ac8 ProSAT]</span></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | |||
</table> | </table> | ||
== Function == | == Function == | ||
[ | [https://www.uniprot.org/uniprot/CCPR_YEAST CCPR_YEAST] Destroys radicals which are normally produced within the cells and which are toxic to biological systems. | ||
== 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/ac/1ac8_consurf.spt"</scriptWhenChecked> | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ac/1ac8_consurf.spt"</scriptWhenChecked> | ||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/ | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=1ac8 ConSurf]. | ||
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
| Line 24: | Line 24: | ||
Conformational changes that gate the access of substrates or ligands to an active site are important features of enzyme function. In this report, we describe an unusual example of a structural rearrangement near a buried artificial cavity in cytochrome c peroxidase that occurs on binding protonated benzimidazole. A hinged main-chain rotation at two residues (Pro 190 and Asn 195) results in a surface loop rearrangement that opens a large solvent-accessible channel for the entry of ligands to an otherwise inaccessible binding site. The trapping of this alternate conformational state provides a unique view of the extent to which protein dynamics can allow small molecule penetration into buried protein cavities. | Conformational changes that gate the access of substrates or ligands to an active site are important features of enzyme function. In this report, we describe an unusual example of a structural rearrangement near a buried artificial cavity in cytochrome c peroxidase that occurs on binding protonated benzimidazole. A hinged main-chain rotation at two residues (Pro 190 and Asn 195) results in a surface loop rearrangement that opens a large solvent-accessible channel for the entry of ligands to an otherwise inaccessible binding site. The trapping of this alternate conformational state provides a unique view of the extent to which protein dynamics can allow small molecule penetration into buried protein cavities. | ||
A ligand-gated, hinged loop rearrangement opens a channel to a buried artificial protein cavity.,Fitzgerald MM, Musah RA, McRee DE, Goodin DB Nat Struct Biol. 1996 Jul;3(7):626-31. PMID: | A ligand-gated, hinged loop rearrangement opens a channel to a buried artificial protein cavity.,Fitzgerald MM, Musah RA, McRee DE, Goodin DB Nat Struct Biol. 1996 Jul;3(7):626-31. PMID:008673607<ref>PMID:008673607</ref> | ||
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 1ac8" style="background-color:#fffaf0;"></div> | |||
==See Also== | ==See Also== | ||
*[[Cytochrome c peroxidase|Cytochrome c peroxidase]] | *[[Cytochrome c peroxidase 3D structures|Cytochrome c peroxidase 3D structures]] | ||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: Saccharomyces cerevisiae]] | [[Category: Saccharomyces cerevisiae]] | ||
[[Category: Bunte | [[Category: Bunte SW]] | ||
[[Category: Goodin | [[Category: Goodin DB]] | ||
[[Category: Jensen | [[Category: Jensen GM]] | ||
[[Category: Mcree | [[Category: Mcree DE]] | ||
[[Category: Musah | [[Category: Musah RA]] | ||
[[Category: Rosenfeld | [[Category: Rosenfeld R]] | ||
