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1aa4

From Proteopedia

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[[Image:1aa4.gif|left|200px]]
 
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{{Structure
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==SPECIFICITY OF LIGAND BINDING IN A BURIED POLAR CAVITY OF CYTOCHROME C PEROXIDASE==
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|PDB= 1aa4 |SIZE=350|CAPTION= <scene name='initialview01'>1aa4</scene>, resolution 2.1&Aring;
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<StructureSection load='1aa4' size='340' side='right'caption='[[1aa4]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
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|SITE= <scene name='pdbsite=ACT:Removal+Of+TRP+191+Forms+An+Internal+Cavity+Below+The+He+...'>ACT</scene>
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>
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<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>
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|ACTIVITY= <span class='plainlinks'>[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] </span>
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</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>
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|GENE= CCP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])
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<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>
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|DOMAIN=
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<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>
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|RELATEDENTRY=
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1aa4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1aa4 OCA], [http://www.ebi.ac.uk/pdbsum/1aa4 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1aa4 RCSB]</span>
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== Function ==
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}}
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[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.
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/aa/1aa4_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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'''SPECIFICITY OF LIGAND BINDING IN A BURIED POLAR CAVITY OF CYTOCHROME C PEROXIDASE'''
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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>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 1aa4" style="background-color:#fffaf0;"></div>
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==Overview==
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==See Also==
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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.
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*[[Cytochrome c peroxidase 3D structures|Cytochrome c peroxidase 3D structures]]
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== References ==
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==About this Structure==
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<references/>
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1AA4 is a [[Single protein]] structure of sequence from [http://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].
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__TOC__
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</StructureSection>
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==Reference==
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[[Category: Large Structures]]
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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://www.ncbi.nlm.nih.gov/pubmed/8673607 8673607]
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[[Category: Cytochrome-c peroxidase]]
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[[Category: Saccharomyces cerevisiae]]
[[Category: Saccharomyces cerevisiae]]
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[[Category: Single protein]]
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[[Category: Fitzgerald MM]]
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[[Category: Fitzgerald, M M.]]
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[[Category: Goodin DB]]
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[[Category: Goodin, D B.]]
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[[Category: Mcree DE]]
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[[Category: Mcree, D E.]]
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[[Category: Musah RA]]
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[[Category: Musah, R A.]]
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[[Category: oxidoreductase]]
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[[Category: peroxidase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 18:36:32 2008''
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Current revision

SPECIFICITY OF LIGAND BINDING IN A BURIED POLAR CAVITY OF CYTOCHROME C PEROXIDASE

PDB ID 1aa4

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