2ia8: Difference between revisions

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-[[Image:2ia8.jpg|left|200px]]
- {{Structure
+==Kinetic and Crystallographic Studies of a Redesigned Manganese-Binding Site in Cytochrome c Peroxidase==
-|PDB= 2ia8 |SIZE=350|CAPTION= <scene name='initialview01'>2ia8</scene>, resolution 1.48&Aring;
+<StructureSection load='2ia8' size='340' side='right'caption='[[2ia8]], [[Resolution|resolution]] 1.48&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=HEM:PROTOPORPHYRIN IX CONTAINING FE'>HEM</scene>
+<table><tr><td colspan='2'>[[2ia8]] 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=2IA8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2IA8 FirstGlance]. <br>
-|ACTIVITY= [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]
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.48&#8491;</td></tr>
-|GENE= CCP1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])
+<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=2ia8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ia8 OCA], [https://pdbe.org/2ia8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ia8 RCSB], [https://www.ebi.ac.uk/pdbsum/2ia8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ia8 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/ia/2ia8_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=2ia8 ConSurf].
+<div style="clear:both"></div>
-'''Kinetic and Crystallographic Studies of a Redesigned Manganese-Binding Site in Cytochrome c Peroxidase'''
+==See Also==
+*[[Cytochrome c peroxidase 3D structures|Cytochrome c peroxidase 3D structures]]
+__TOC__
-==Overview==
+</StructureSection>
-Manganese peroxidase (MnP) from the white rot fungus Phanerochaete chrysosporium contains a manganese-binding site that plays a critical role in its function. Previously, a Mn(II)-binding site was designed into cytochrome c peroxidase (CcP) based on sequence homology (Yeung et al. in Chem. Biol. 4:215-222, 1997; Gengenbach et al. in Biochemistry 38:11425-11432, 1999). Here, we report a redesign of this site based on X-ray structural comparison of MnP and CcP. The variant, CcP(D37E, V45E, H181E), displays 2.5-fold higher catalytic efficiency (k (cat)/K (M)) than the variant in the original design, mostly due to a stronger K (M) of 1.9 mM (vs. 4.1 mM). High-resolution X-ray crystal structures of a metal-free form and a form with Co(II) at the designed Mn(II) site were also obtained. The metal ion in the engineered metal-binding site overlays well with Mn(II) bound in MnP, suggesting that this variant is the closest structural model of the Mn(II)-binding site in MnP for which a crystal structure exists. A major difference arises in the distances of the ligands to the metal; the metal-ligand interactions in the CcP variant are much weaker than the corresponding interactions in MnP, probably owing to partial occupancy of metal ion at the designed site, difference in the identity of metal ions (Co(II) rather than Mn(II)) and other interactions in the second coordination sphere. These results indicate that the metal ion, the ligands, and the environment around the metal-binding site play important roles in tuning the structure and function of metalloenzymes.
+[[Category: Large Structures]]
-==About this Structure==
-IA8 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=2IA8 OCA].
-==Reference==
-Kinetic and crystallographic studies of a redesigned manganese-binding site in cytochrome c peroxidase., Pfister TD, Mirarefi AY, Gengenbach AJ, Zhao X, Danstrom C, Conatser N, Gao YG, Robinson H, Zukoski CF, Wang AH, Lu Y, J Biol Inorg Chem. 2007 Jan;12(1):126-37. Epub 2006 Oct 5. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17021923 17021923]
-[[Category: Cytochrome-c peroxidase]]
 [[Category: Saccharomyces cerevisiae]]
-[[Category: Single protein]]
+[[Category: Conaster CDN]]
-[[Category: Conaster, C D.N.]]
+[[Category: Gao YG]]
-[[Category: Gao, Y G.]]
+[[Category: Gengenbach AJ]]
-[[Category: Gengenbach, A J.]]
+[[Category: Lu Y]]
-[[Category: Lu, Y.]]
+[[Category: Mirarefi AY]]
-[[Category: Mirarefi, A Y.]]
+[[Category: Pfister T]]
-[[Category: Pfister, T.]]
+[[Category: Robinson H]]
-[[Category: Robinson, H.]]
+[[Category: Wang AHJ]]
-[[Category: Wang, A H.J.]]
+[[Category: Zhao X]]
-[[Category: Zhao, X.]]
+[[Category: Zukoski CF]]
-[[Category: Zukoski, C F.]]
-[[Category: HEM]]
-[[Category: biomimetic]]
-[[Category: manganese oxidation]]
-[[Category: metal-binding site]]
-[[Category: metalloprotein]]
-[[Category: oxidoreductase]]
-[[Category: protein engineering]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 17:27:06 2008''