1ML2

Crystal Structure of a Mutant Variant of Cytochrome c Peroxidase with Zn(II)-(20-oxo-Protoporphyrin IX)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.183 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

A Novel Heme and Peroxide-Dependent Tryptophan-Tyrosine Cross-Link in a Mutant of Cytochrome c Peroxidase

Bhaskar, B.Immoos, C.E.Shimizu, H.Sulc, F.Farmer, P.J.Poulos, T.L.

(2003) J Mol Biol 328: 157-166

  • DOI: 10.1016/s0022-2836(03)00179-7
  • Primary Citation of Related Structures:  
    1MK8, 1MKR, 1MKQ, 1ML2

  • PubMed Abstract: 
  • The crystal structure of a cytochrome c peroxidase mutant where the distal catalytic His52 is converted to Tyr reveals that the tyrosine side-chain forms a covalent bond with the indole ring nitrogen atom of Trp51. We hypothesize that this novel bond results from peroxide activation by the heme iron followed by oxidation of Trp51 and Tyr52 ...

    The crystal structure of a cytochrome c peroxidase mutant where the distal catalytic His52 is converted to Tyr reveals that the tyrosine side-chain forms a covalent bond with the indole ring nitrogen atom of Trp51. We hypothesize that this novel bond results from peroxide activation by the heme iron followed by oxidation of Trp51 and Tyr52. This hypothesis has been tested by incorporation of a redox-inactive Zn-protoporphyrin into the protein, and the resulting crystal structure shows the absence of a Trp51-Tyr52 cross-link. Instead, the Tyr52 side-chain orients away from the heme active-site pocket, which requires a substantial rearrangement of residues 72-80 and 134-144. Additional experiments where heme-containing crystals of the mutant were treated with peroxide support our hypothesis that this novel Trp-Tyr cross-link is a peroxide-dependent process mediated by the heme iron.


    Organizational Affiliation

    Department of Molecular Biology and Biochemistry, School of Biological Sciences, University of California, Irvine, CA 92697-3900, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c PeroxidaseA294Saccharomyces cerevisiaeMutation(s): 1 
Gene Names: OPBYC
EC: 1.11.1.5
UniProt
Find proteins for P00431 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P00431 
Go to UniProtKB:  P00431
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZEM (Subject of Investigation/LOI)
Query on ZEM

Download Ideal Coordinates CCD File 
B [auth A]20-OXO-PROTOPORPHYRIN IX CONTAINING ZN(II)
C34 H32 N4 O5 Zn
GKGQUBKNYNPVCL-ZALNKZPHDI
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.183 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.487α = 90
b = 50.998β = 90
c = 118.759γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
X-GENdata reduction
AMoREphasing
CNSrefinement
X-GENdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-04-08
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description