5XKV

structure of sperm whale myoglobin F138W


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.163 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Rational design of artificial dye-decolorizing peroxidases using myoglobin by engineering Tyr/Trp in the heme center

Li, L.L.Yuan, H.Liao, F.He, B.Gao, S.Q.Wen, G.B.Tan, X.Lin, Y.W.

(2017) Dalton Trans 46: 11230-11238

  • DOI: https://doi.org/10.1039/c7dt02302b
  • Primary Citation of Related Structures:  
    5XKV, 5XKW

  • PubMed Abstract: 

    The rational design of metalloenzymes provides advantages not only for illustrating the structure and function relationship of native enzymes, but also for creating functional artificial enzymes comparable to native enzymes. Dye-decolorizing peroxidases (DyPs) are a new family of heme peroxidases and have received much attention recently. Inspired by the structural features of native DyPs with multiple Tyr and Trp residues, we herein aimed to design functional artificial DyPs using myoglobin (Mb), an O 2 carrier as a protein scaffold, by further introduction of Tyr/Trp into the secondary sphere of the heme center in the F43Y Mb mutant. The latter has been shown to possess a novel Tyr-heme cross-link and exhibit enhanced peroxidase activity, which provides an ideal platform to design a series of derivatives, including F43Y/F46Y Mb, F43Y/I107Y Mb, F43Y/F138 W Mb and F43Y/I107Y/F138 W Mb. Our design revealed that the Tyr-heme cross-link was well-retained in the mutants except for F43Y/F46Y Mb, as confirmed by X-ray crystal structure analysis. More importantly, stopped-flow kinetic studies showed that these derivatives exhibit enhanced dye-decolorizing peroxidase activities compared to that of wild-type (WT) Mb. This is particularly the case for the double mutant F43Y/F138 W Mb, exhibiting an overall catalytic efficiency (k cat /K m ) of 110 670 M -1 s -1 , which is ∼144-fold and ∼20-fold that of WT Mb and F43Y Mb, respectively, and is ∼4.3-fold that of native DyP from Vibrio cholerae. Stopped-flow, electron paramagnetic resonance (EPR) and isothermal titration calorimetry (ITC) studies further provided insights into the activation of H 2 O 2 and the binding of a substrate, reactive blue 19 (RB19), to the double mutant. This study provides valuable information for elucidating the structure and dye-decolorizing function relationship of peroxidases, and also clues for the design of other functional artificial heme enzymes.


  • Organizational Affiliation

    School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China. linlinying@hotmail.com ywlin@usc.edu.cn.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Myoglobin153Physeter catodonMutation(s): 1 
Gene Names: MB
UniProt
Find proteins for P02185 (Physeter macrocephalus)
Explore P02185 
Go to UniProtKB:  P02185
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02185
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
B [auth A]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.163 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.766α = 90
b = 48.441β = 90
c = 78.898γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data processing
HKL-2000data scaling
MOLREPphasing
HKL-3000data reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2018-05-16 
  • Deposition Author(s): Yuan, H.

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-16
    Type: Initial release
  • Version 1.1: 2018-05-30
    Changes: Data collection, Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description