2GHZ

Crystal structure of Azurin Phe114Pro mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.142 
  • R-Value Observed: 0.144 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The role of hydrogen bonding at the active site of a cupredoxin: the Phe114Pro azurin variant.

Yanagisawa, S.Banfield, M.J.Dennison, C.

(2006) Biochemistry 45: 8812-8822

  • DOI: 10.1021/bi0606851
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The Phe114Pro mutation to the cupredoxin azurin (AZ) leads to a number of structural changes at the active site attributed to deletion of one of the hydrogen bonds to the Cys112 ligand, removal of the bulky phenyl group from the hydrophobic patch of ...

    The Phe114Pro mutation to the cupredoxin azurin (AZ) leads to a number of structural changes at the active site attributed to deletion of one of the hydrogen bonds to the Cys112 ligand, removal of the bulky phenyl group from the hydrophobic patch of the protein, and steric interactions made by the introduced Pro. The remaining hydrogen bond between the coordinating thiolate and the backbone amide of Asn47 is strengthened. At the type-1 copper site, the Cu(II)-O(Gly45) axial interaction decreases, while the metal moves out of the plane formed by the equatorial His46, Cys112, and His117 ligands, shortening the bond to the axially coordinating Met121. The resulting distorted tetrahedral geometry is distinct from the trigonal bipyramidal arrangement in the wild-type (WT) protein. The unique position of the main S(Cys) --> Cu(II) ligand-to-metal charge-transfer transition in AZ (628 nm) has shifted in the Phe114Pro variant to a value that is more typical for cupredoxins (599 nm). This probably occurs because of the removal of the Phe114-Cys112 hydrogen bond. The Phe114Pro mutation results in a 90 mV decrease in the reduction potential of AZ, and removal of the second hydrogen bond to the Cys ligand seems to be the major cause of this change. The C-terminal His117 ligand does not protonate in the reduced Phe114Pro AZ variant, which suggests that none of the structural features altered by the mutation are responsible for the absence of this effect in the WT protein. Upon reduction, the copper displaces further from the equatorial ligand plane and the Cu-S(Met121) bond length decreases. These changes are larger than those seen in the WT protein and contribute to the order of magnitude decrease in the intrinsic electron-transfer capabilities of the Phe114Pro variant.


    Organizational Affiliation

    Institute for Cell and Molecular Biosciences, Medical School, University of Newcastle upon Tyne, Newcastle upon Tyne NE2 4HH, United Kingdom.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
AzurinA, B128Pseudomonas aeruginosaMutation(s): 1 
Gene Names: azu
Find proteins for P00282 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore P00282 
Go to UniProtKB:  P00282
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CU
Query on CU

Download CCD File 
A, B
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.142 
  • R-Value Observed: 0.144 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.35α = 90
b = 47.81β = 90
c = 132.52γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-07-04
    Type: Initial release
  • Version 1.1: 2008-02-06
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance