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Kinetic and crystallographic studies of a redesigned manganese-binding site in cytochrome c peroxidase

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Abstract

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 MnII-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 CoII at the designed MnII site were also obtained. The metal ion in the engineered metal-binding site overlays well with MnII bound in MnP, suggesting that this variant is the closest structural model of the MnII-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 (CoII rather than MnII) 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.

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Abbreviations

CcP:

Cytochrome c peroxidase from Saccharomyces cerevisiae

CcP(MI):

Recombinant yeast CcP containing Met-Ile at the N-terminus in addition to the normal wild-type yeast CcP sequence

EPR:

Electron paramagnetic resonance

Compound I:

Ferryl (FeIV-oxo) heme and porphyrin cation radical

Compound I•:

Ferryl (FeIV-oxo) heme and Trp radical

Compound II:

Ferryl (FeIV-oxo) heme

MnCcP:

CcP(G41E, V45E, H181D)

MnCcP2:

CcP(G41E, V45E, W51F, H181D, W191F)

MnCcP.1:

CcP(D37E, V45E, H181E)

MnP:

Manganese peroxidase

MP6.8:

CcP(D37E, P44D, V45D)

PC:

Phanerochaete chrysosporium

WTCcP:

Wild-type yeast CcP

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Acknowledgements

This material is based upon work supported by the National Institute of General Medical Sciences in the National Institute of Health (GM62211 to Y.L.).

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Authors and Affiliations

  1. Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave, Urbana, IL, 61801, USA

    Thomas D. Pfister & Yi Lu

  2. Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA

    Amir Y. Mirarefi & Charles F. Zukoski

  3. Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA

    Alan J. Gengenbach, Xuan Zhao, Connor Danstrom, Nicole Conatser & Yi Lu

  4. School of Chemical Sciences Biocrystallization Service, University of Illinois at Urbana-Champaign, Urbana, IL, USA

    Yi-Gui Gao

  5. Department of Biology, Brookhaven National Laboratory, Upton, NY, USA

    Howard Robinson

  6. Institute of Biological Chemistry and Core Facility for Protein Crystallography, Academia Sinica, Nankang, Taipei, Taiwan

    Andrew H.-J. Wang

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  1. Thomas D. Pfister
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  11. Yi Lu
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Correspondence to Yi Lu.

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Pfister, T.D., Mirarefi, A.Y., Gengenbach, A.J. et al. Kinetic and crystallographic studies of a redesigned manganese-binding site in cytochrome c peroxidase. J Biol Inorg Chem 12, 126–137 (2007). https://doi.org/10.1007/s00775-006-0171-0

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  • DOI: https://doi.org/10.1007/s00775-006-0171-0

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