2ia8: Difference between revisions

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-[[Image:2ia8.jpg|left|200px]]<br /><applet load="2ia8" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="2ia8, resolution 1.48&Aring;" />
-'''Kinetic and Crystallographic Studies of a Redesigned Manganese-Binding Site in Cytochrome c Peroxidase'''<br />
-==Overview==
+==Kinetic and Crystallographic Studies of a Redesigned Manganese-Binding Site in Cytochrome c Peroxidase==
-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.
+<StructureSection load='2ia8' size='340' side='right'caption='[[2ia8]], [[Resolution|resolution]] 1.48&Aring;' scene=''>
+== Structural highlights ==
+<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>
+</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>
+<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>
-==About this Structure==
+==See Also==
-IA8 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] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IA8 OCA].
+*[[Cytochrome c peroxidase 3D structures|Cytochrome c peroxidase 3D structures]]
+__TOC__
-==Reference==
+</StructureSection>
-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://ispc.weizmann.ac.il//pmbin/getpm?pmid=17021923 17021923]
+[[Category: Large Structures]]
-[[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 Wed Jan 23 13:51:48 2008''