8K9N

Subatomic resolution structure of Pseudoazurin from Alcaligenes faecalis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.86 Å
  • R-Value Free: 0.163 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.145 

Starting Model: experimental
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Literature

Overlooked Hydrogen Bond in a Blue Copper Protein Uncovered by Neutron and Sub- angstrom ngstrom Resolution X-ray Crystallography.

Fukuda, Y.Lintuluoto, M.Kurihara, K.Hasegawa, K.Inoue, T.Tamada, T.

(2024) Biochemistry 63: 339-347

  • DOI: https://doi.org/10.1021/acs.biochem.3c00517
  • Primary Citation of Related Structures:  
    8K9N, 8K9P

  • PubMed Abstract: 

    Metalloproteins play fundamental roles in organisms and are utilized as starting points for the directed evolution of artificial enzymes. Knowing the strategies of metalloproteins, by which they exquisitely tune their activities, will not only lead to an understanding of biochemical phenomena but also contribute to various applications. The blue copper protein (BCP) has been a renowned model system to understand the biology, chemistry, and physics of metalloproteins. Pseudoazurin (Paz), a blue copper protein, mediates electron transfer in the bacterial anaerobic respiratory chain. Its redox potential is finely tuned by hydrogen (H) bond networks; however, difficulty in visualizing H atom positions in the protein hinders the detailed understanding of the protein's structure-function relationship. We here used neutron and sub-ångström resolution X-ray crystallography to directly observe H atoms in Paz. The 0.86-Å-resolution X-ray structure shows that the peptide bond between Pro80 and the His81 Cu ligand deviates from the ideal planar structure. The 1.9-Å-resolution neutron structure confirms a long-overlooked H bond formed by the amide of His81 and the S atom of another Cu ligand Cys78. Quantum mechanics/molecular mechanics calculations show that this H bond increases the redox potential of the Cu site and explains the experimental results well. Our study demonstrates the potential of neutron and sub-ångström resolution X-ray crystallography to understand the chemistry of metalloproteins at atomic and quantum levels.


  • Organizational Affiliation

    Graduate School of Pharmaceutical Science, Osaka University, Suita 565-0871, Osaka, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pseudoazurin126Alcaligenes faecalisMutation(s): 0 
UniProt
Find proteins for P04377 (Alcaligenes faecalis)
Explore P04377 
Go to UniProtKB:  P04377
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04377
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.86 Å
  • R-Value Free: 0.163 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.145 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.676α = 90
b = 49.676β = 90
c = 96.519γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan--

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-14
    Type: Initial release
  • Version 1.1: 2024-02-21
    Changes: Database references