1BVA

MANGANESE BINDING MUTANT IN CYTOCHROME C PEROXIDASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Observed: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Rational design of a functional metalloenzyme: introduction of a site for manganese binding and oxidation into a heme peroxidase.

Wilcox, S.K.Putnam, C.D.Sastry, M.Blankenship, J.Chazin, W.J.McRee, D.E.Goodin, D.B.

(1998) Biochemistry 37: 16853-16862

  • DOI: 10.1021/bi9815039
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The design of a series of functionally active models for manganese peroxidase (MnP) is described. Artificial metal binding sites were created near the heme of cytochrome c peroxidase (CCP) such that one of the heme propionates could serve as a metal ...

    The design of a series of functionally active models for manganese peroxidase (MnP) is described. Artificial metal binding sites were created near the heme of cytochrome c peroxidase (CCP) such that one of the heme propionates could serve as a metal ligand. At least two of these designs, MP6.1 and MP6.8, bind Mn2+ with Kd congruent with 0.2 mM, react with H2O2 to form stable ferryl heme species, and catalyze the steady-state oxidation of Mn2+ at enhanced rates relative to WT CCP. The kinetic parameters for this activity vary considerably in the presence of various dicarboxylic acid chelators, suggesting that the similar features displayed by native MnP are largely intrinsic to the manganese oxidation reaction rather than due to a specific interaction between the chelator and enzyme. Analysis of pre-steady-state data shows that electron transfer from Mn2+ to both the Trp-191 radical and the ferryl heme center of compound ES is enhanced by the metal site mutations, with transfer to the ferryl center showing the greatest stimulation. These properties are perplexingly similar to those reported for an alternate model for this site (1), despite rather distinct features of the two designs. Finally, we have determined the crystal structure at 1.9 A of one of our designs, MP6.8, in the presence of MnSO4. A weakly occupied metal at the designed site appears to coordinate two of the proposed ligands, Asp-45 and the heme 7-propionate. Paramagnetic nuclear magnetic resonance spectra also suggest that Mn2+ is interacting with the heme 7-propionate in MP6.8. The structure provides a basis for understanding the similar results of Yeung et al. (1), and suggests improvements for future designs.


    Organizational Affiliation

    Department of Molecular Biology, MB8, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (CYTOCHROME C PEROXIDASE)A294Saccharomyces cerevisiaeMutation(s): 3 
Gene Names: CCP (MKT)
EC: 1.11.1.5
Find proteins for P00431 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P00431 
Go to UniProtKB:  P00431
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
MN
Query on MN

Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Observed: 0.179 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.8α = 90
b = 73.6β = 90
c = 50.5γ = 90
Software Package:
Software NamePurpose
SHELXL-97refinement
XTALVIEWrefinement
X-GENdata reduction
X-GENdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-12-23
    Type: Initial release
  • Version 1.1: 2007-10-16
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description
  • Version 1.4: 2019-07-24
    Changes: Data collection, Refinement description