2cyp

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[[Image:2cyp.jpg|left|200px]]
 
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==Crystal structure of yeast cytochrome C peroxidase refined at 1.7-angstroms resolution==
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The line below this paragraph, containing "STRUCTURE_2cyp", creates the "Structure Box" on the page.
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<StructureSection load='2cyp' size='340' side='right'caption='[[2cyp]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[2cyp]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1cyp 1cyp]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CYP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2CYP FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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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]] 1.7&#8491;</td></tr>
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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>, <scene name='pdbligand=O:OXYGEN+ATOM'>O</scene></td></tr>
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{{STRUCTURE_2cyp| PDB=2cyp | SCENE= }}
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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=2cyp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2cyp OCA], [https://pdbe.org/2cyp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2cyp RCSB], [https://www.ebi.ac.uk/pdbsum/2cyp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2cyp ProSAT]</span></td></tr>
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</table>
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== Function ==
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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/cy/2cyp_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=2cyp ConSurf].
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<div style="clear:both"></div>
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'''Crystal structure of yeast cytochrome C peroxidase refined at 1.7-angstroms resolution'''
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==See Also==
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*[[Cytochrome c peroxidase 3D structures|Cytochrome c peroxidase 3D structures]]
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__TOC__
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==Overview==
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</StructureSection>
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The crystal structure of cytochrome c peroxidase (EC 1.11.1.5) has been refined to an R factor of 0.20 computed for all reflections to 1.7 A. The refined molecular model includes 263 bound water molecules and allows for x-ray scattering by amorphous solvent. The mean positional error in atomic coordinates is estimated to lie between 0.12 and 0.21 A. Two factors are identified which may account for the ability of the enzyme to stabilize high-oxidation states of the heme iron during catalysis: 1) the proximal histidine forms a hydrogen bond with a buried aspartic acid side chain, Asp-235; and 2) the heme environment is more polar than in the cytochromes c or globins, owing to the presence of the partially buried side-chain of Arg-48 and five water molecules bound in close proximity to the heme. Two of these occupy the presumed peroxide-binding site. Two candidates are likely for the side chain that is oxidized to a free radical during formation of Compound I: 1) Trp-51, which rests 3.3 A above the heme plane in close proximity (2.7 A) to the sixth coordination position; and 2) Met-172, which is 3.7 A from the heme. Nucleophilic stabilization of the methionyl cation radical may be possible via Asp-235. His-181 is found to lie coplanar with the heme in a niche between the two propionates near the suspected cytochrome c-binding site. A network of hydrogen bonds involving this histidine may provide a preferred pathway for electron transfer between hemes.
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[[Category: Large Structures]]
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==About this Structure==
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2CYP is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1cyp 1cyp]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CYP OCA].
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==Reference==
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Crystal structure of yeast cytochrome c peroxidase refined at 1.7-A resolution., Finzel BC, Poulos TL, Kraut J, J Biol Chem. 1984 Nov 10;259(21):13027-36. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/6092361 6092361]
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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: Finzel BC]]
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[[Category: Finzel, B C.]]
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[[Category: Kraut J]]
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[[Category: Kraut, J.]]
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[[Category: Poulos TL]]
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[[Category: Poulos, T L.]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 23:21:52 2008''
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Current revision

Crystal structure of yeast cytochrome C peroxidase refined at 1.7-angstroms resolution

PDB ID 2cyp

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