4P5S

Structure of reduced W45Y mutant of amicyanin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.02 Å
  • R-Value Free: 0.150 
  • R-Value Work: 0.134 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

The sole tryptophan of amicyanin enhances its thermal stability but does not influence the electronic properties of the type 1 copper site.

Dow, B.A.Sukumar, N.Matos, J.O.Choi, M.Schulte, A.Tatulian, S.A.Davidson, V.L.

(2014) Arch.Biochem.Biophys. 550-551: 20-27

  • DOI: 10.1016/j.abb.2014.03.010
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The cupredoxin amicyanin possesses a single tryptophan residue, Trp45. Its fluorescence is quenched when copper is bound even though it is separated by 10.1Å. Mutation of Trp45 to Ala, Phe, Leu and Lys resulted in undetectable protein expression. A W ...

    The cupredoxin amicyanin possesses a single tryptophan residue, Trp45. Its fluorescence is quenched when copper is bound even though it is separated by 10.1Å. Mutation of Trp45 to Ala, Phe, Leu and Lys resulted in undetectable protein expression. A W45Y amicyanin variant was isolated. The W45Y mutation did not alter the spectroscopic properties or intrinsic redox potential of amicyanin, but increased the pKa value for the pH-dependent redox potential by 0.5 units. This is due to a hydrogen-bond involving the His95 copper ligand which is present in reduced W45Y amicyanin but not in native amicyanin. The W45Y mutation significantly decreased the thermal stability of amicyanin, as determined by changes in the visible absorbance of oxidized amicyanin and in the circular dichroism spectra for oxidized, reduced and apo forms of amicyanin. Comparison of the crystal structures suggests that the decreased stability of W45Y amicyanin may be attributed to the loss of a strong interior hydrogen bond between Trp45 and Tyr90 in native amicyanin which links two of the β-sheets that comprise the overall structure of amicyanin. Thus, Trp45 is critical for stabilizing the structure of amicyanin but it does not influence the electronic properties of the copper which quenches its fluorescence.


    Organizational Affiliation

    Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL 32827, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Amicyanin
A
105Paracoccus denitrificansMutation(s): 1 
Gene Names: mauC (ami)
Find proteins for P22364 (Paracoccus denitrificans)
Go to UniProtKB:  P22364
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CU1
Query on CU1

Download SDF File 
Download CCD File 
A
COPPER (I) ION
Cu
VMQMZMRVKUZKQL-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.02 Å
  • R-Value Free: 0.150 
  • R-Value Work: 0.134 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 27.165α = 90.00
b = 56.646β = 96.67
c = 28.663γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PDB_EXTRACTdata extraction
PHENIXrefinement
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM103403

Revision History 

  • Version 1.0: 2014-04-23
    Type: Initial release
  • Version 1.1: 2014-10-01
    Type: Database references
  • Version 2.0: 2017-09-13
    Type: Advisory, Author supporting evidence, Database references, Derived calculations, Non-polymer description, Other, Source and taxonomy, Structure summary