5HAV

Sperm whale myoglobin mutant L29H F33Y F43H (F33Y CuBMb) with oxygen bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.268 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.146 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Spectroscopic and Crystallographic Evidence for the Role of a Water-Containing H-Bond Network in Oxidase Activity of an Engineered Myoglobin.

Petrik, I.D.Davydov, R.Ross, M.Zhao, X.Hoffman, B.Lu, Y.

(2016) J.Am.Chem.Soc. 138: 1134-1137

  • DOI: 10.1021/jacs.5b12004

  • PubMed Abstract: 
  • Heme-copper oxidases (HCOs) catalyze efficient reduction of oxygen to water in biological respiration. Despite progress in studying native enzymes and their models, the roles of non-covalent interactions in promoting this activity are still not well ...

    Heme-copper oxidases (HCOs) catalyze efficient reduction of oxygen to water in biological respiration. Despite progress in studying native enzymes and their models, the roles of non-covalent interactions in promoting this activity are still not well understood. Here we report EPR spectroscopic studies of cryoreduced oxy-F33Y-CuBMb, a functional model of HCOs engineered in myoglobin (Mb). We find that cryoreduction at 77 K of the O2-bound form, trapped in the conformation of the parent oxyferrous form, displays a ferric-hydroperoxo EPR signal, in contrast to the cryoreduced oxy-wild-type (WT) Mb, which is unable to deliver a proton and shows a signal from the peroxo-ferric state. Crystallography of oxy-F33Y-CuBMb reveals an extensive H-bond network involving H2O molecules, which is absent from oxy-WTMb. This H-bonding proton-delivery network is the key structural feature that transforms the reversible oxygen-binding protein, WTMb, into F33Y-CuBMb, an oxygen-activating enzyme that reduces O2 to H2O. These results provide direct evidence of the importance of H-bond networks involving H2O in conferring enzymatic activity to a designed protein. Incorporating such extended H-bond networks in designing other metalloenzymes may allow us to confer and fine-tune their enzymatic activities.


    Organizational Affiliation

    Department of Chemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Myoglobin
A
153Physeter catodonMutation(s): 3 
Gene Names: MB
Find proteins for P02185 (Physeter catodon)
Go to Gene View: MB
Go to UniProtKB:  P02185
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OXY
Query on OXY

Download SDF File 
Download CCD File 
A
OXYGEN MOLECULE
O2
MYMOFIZGZYHOMD-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

Download SDF File 
Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.268 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.146 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 39.632α = 90.00
b = 47.609β = 90.00
c = 76.534γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2015-12-31 
  • Released Date: 2016-01-13 
  • Deposition Author(s): Petrik, I.D., Lu, Y.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM062211

Revision History 

  • Version 1.0: 2016-01-13
    Type: Initial release
  • Version 1.1: 2016-02-03
    Type: Database references
  • Version 1.2: 2016-02-17
    Type: Database references
  • Version 1.3: 2017-09-20
    Type: Author supporting evidence, Derived calculations