2ia8: Difference between revisions

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Revision as of 18:27, 20 March 2008

File:2ia8.jpg

, resolution 1.48Å

Ligands:

Gene:

CCP1 (Saccharomyces cerevisiae)

Activity:

Cytochrome-c peroxidase, with EC number 1.11.1.5

Coordinates:

save as pdb, mmCIF, xml

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

OverviewOverview

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.

About this StructureAbout this Structure

2IA8 is a Single protein structure of sequence from Saccharomyces cerevisiae. Full crystallographic information is available from OCA.

ReferenceReference

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

Page seeded by OCA on Thu Mar 20 17:27:06 2008

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"
+[[Image:2ia8.jpg|left|200px]]
-caption="2ia8, resolution 1.48&Aring;" />
-'''Kinetic and Crystallographic Studies of a Redesigned Manganese-Binding Site in Cytochrome c Peroxidase'''<br />
+ {{Structure
+|PDB= 2ia8 |SIZE=350|CAPTION= <scene name='initialview01'>2ia8</scene>, resolution 1.48&Aring;
+|SITE=
+|LIGAND= <scene name='pdbligand=HEM:PROTOPORPHYRIN IX CONTAINING FE'>HEM</scene>
+|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]
+|GENE= CCP1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])
+}}
+'''Kinetic and Crystallographic Studies of a Redesigned Manganese-Binding Site in Cytochrome c Peroxidase'''
 ==Overview==
@@ Line 7: / Line 16: @@
 ==About this Structure==
-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].
+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://ispc.weizmann.ac.il//pmbin/getpm?pmid=17021923 17021923]
+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]]
@@ Line 32: / Line 41: @@
 [[Category: protein engineering]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 17:50:32 2008''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 17:27:06 2008''