2ia8: Difference between revisions

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<StructureSection load='2ia8' size='340' side='right'caption='[[2ia8]], [[Resolution|resolution]] 1.48&Aring;' scene=''>
<StructureSection load='2ia8' size='340' side='right'caption='[[2ia8]], [[Resolution|resolution]] 1.48&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2ia8]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. 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>
<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='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>
</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='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">CCP1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Cytochrome-c_peroxidase Cytochrome-c peroxidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.5 1.11.1.5] </span></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>
<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>
</table>
== Function ==
== 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.  
[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 ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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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=2ia8 ConSurf].
</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>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.
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:17021923<ref>PMID:17021923</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2ia8" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Cytochrome c peroxidase 3D structures|Cytochrome c peroxidase 3D structures]]
*[[Cytochrome c peroxidase 3D structures|Cytochrome c peroxidase 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Atcc 18824]]
[[Category: Cytochrome-c peroxidase]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Conaster, C D.N]]
[[Category: Saccharomyces cerevisiae]]
[[Category: Gao, Y G]]
[[Category: Conaster CDN]]
[[Category: Gengenbach, A J]]
[[Category: Gao YG]]
[[Category: Lu, Y]]
[[Category: Gengenbach AJ]]
[[Category: Mirarefi, A Y]]
[[Category: Lu Y]]
[[Category: Pfister, T]]
[[Category: Mirarefi AY]]
[[Category: Robinson, H]]
[[Category: Pfister T]]
[[Category: Wang, A H.J]]
[[Category: Robinson H]]
[[Category: Zhao, X]]
[[Category: Wang AHJ]]
[[Category: Zukoski, C F]]
[[Category: Zhao X]]
[[Category: Biomimetic]]
[[Category: Zukoski CF]]
[[Category: Manganese oxidation]]
[[Category: Metal-binding site]]
[[Category: Metalloprotein]]
[[Category: Oxidoreductase]]
[[Category: Protein engineering]]

Latest revision as of 12:02, 21 February 2024

Kinetic and Crystallographic Studies of a Redesigned Manganese-Binding Site in Cytochrome c PeroxidaseKinetic and Crystallographic Studies of a Redesigned Manganese-Binding Site in Cytochrome c Peroxidase

Structural highlights

2ia8 is a 1 chain structure with sequence from Saccharomyces cerevisiae. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.48Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

CCPR_YEAST Destroys radicals which are normally produced within the cells and which are toxic to biological systems.

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

2ia8, resolution 1.48Å

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OCA
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