1aa4: Difference between revisions

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-[[Image:1aa4.gif|left|200px]]<br /><applet load="1aa4" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="1aa4, resolution 2.1&Aring;" />
-'''SPECIFICITY OF LIGAND BINDING IN A BURIED POLAR CAVITY OF CYTOCHROME C PEROXIDASE'''<br />
-==Overview==
+==SPECIFICITY OF LIGAND BINDING IN A BURIED POLAR CAVITY OF CYTOCHROME C PEROXIDASE==
-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.
+<StructureSection load='1aa4' size='340' side='right'caption='[[1aa4]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1aa4]] 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=1AA4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1AA4 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]] 2.1&#8491;</td></tr>
+<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></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=1aa4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1aa4 OCA], [https://pdbe.org/1aa4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1aa4 RCSB], [https://www.ebi.ac.uk/pdbsum/1aa4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1aa4 ProSAT]</span></td></tr>
+</table>
+== 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 ==
+[[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/aa/1aa4_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=1aa4 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+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.
-==About this Structure==
+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:8673607<ref>PMID:8673607</ref>
-AA4 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae] with <scene name='pdbligand=HEM:'>HEM</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Cytochrome-c_peroxidase Cytochrome-c peroxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.5 1.11.1.5] Known structural/functional Site: <scene name='pdbsite=ACT:Removal+Of+TRP+191+Forms+An+Internal+Cavity+Below+The+He+...'>ACT</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AA4 OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8673607 8673607]
+</div>
-[[Category: Cytochrome-c peroxidase]]
+<div class="pdbe-citations 1aa4" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Cytochrome c peroxidase 3D structures|Cytochrome c peroxidase 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Saccharomyces cerevisiae]]
-[[Category: Single protein]]
+[[Category: Fitzgerald MM]]
-[[Category: Fitzgerald, M.M.]]
+[[Category: Goodin DB]]
-[[Category: Goodin, D.B.]]
+[[Category: Mcree DE]]
-[[Category: Mcree, D.E.]]
+[[Category: Musah RA]]
-[[Category: Musah, R.A.]]
-[[Category: HEM]]
-[[Category: oxidoreductase]]
-[[Category: peroxidase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Feb  3 09:29:40 2008''