5HAV | pdb_00005hav

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.27 Å
  • R-Value Free: 
    0.178 (Depositor), 0.178 (DCC) 
  • R-Value Work: 
    0.146 (Depositor), 0.147 (DCC) 
  • R-Value Observed: 
    0.148 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.5 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: https://doi.org/10.1021/jacs.5b12004
  • Primary Citation Related Structures: 
    5HAV

  • 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 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.

Macromolecule Content 

  • Total Structure Weight: 17.92 kDa 
  • Atom Count: 1,565 
  • Modeled Residue Count: 153 
  • Deposited Residue Count: 153 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Myoglobin153Physeter macrocephalusMutation(s): 3 
Gene Names: MB
EC: 1.11.1 (UniProt), 1.7 (UniProt)
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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.27 Å
  • R-Value Free:  0.178 (Depositor), 0.178 (DCC) 
  • R-Value Work:  0.146 (Depositor), 0.147 (DCC) 
  • R-Value Observed: 0.148 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.632α = 90
b = 47.609β = 90
c = 76.534γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM062211

Revision History  (Full details and data files)

  • Version 1.0: 2016-01-13
    Type: Initial release
  • Version 1.1: 2016-02-03
    Changes: Database references
  • Version 1.2: 2016-02-17
    Changes: Database references
  • Version 1.3: 2017-09-20
    Changes: Author supporting evidence, Derived calculations
  • Version 1.4: 2019-12-25
    Changes: Author supporting evidence
  • Version 1.5: 2023-09-27
    Changes: Data collection, Database references, Refinement description