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 
  • R-Value Observed: 0.135 

wwPDB Validation   3D Report Full Report


This is version 2.2 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: https://doi.org/10.1016/j.abb.2014.03.010
  • Primary Citation of Related Structures:  
    4P5R, 4P5S

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Amicyanin105Paracoccus denitrificansMutation(s): 1 
Gene Names: mauCami
UniProt
Find proteins for P22364 (Paracoccus denitrificans)
Explore P22364 
Go to UniProtKB:  P22364
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22364
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CU1
Query on CU1

Download Ideal Coordinates CCD File 
B [auth A]COPPER (I) ION
Cu
VMQMZMRVKUZKQL-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.02 Å
  • R-Value Free: 0.150 
  • R-Value Work: 0.134 
  • R-Value Observed: 0.135 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 27.165α = 90
b = 56.646β = 96.67
c = 28.663γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
PHENIXrefinement
PDB_EXTRACTdata extraction
PHENIXrefinement

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM103403

Revision History  (Full details and data files)

  • Version 1.0: 2014-04-23
    Type: Initial release
  • Version 1.1: 2014-10-01
    Changes: Database references
  • Version 2.0: 2017-09-13
    Changes: Advisory, Author supporting evidence, Database references, Derived calculations, Non-polymer description, Other, Source and taxonomy, Structure summary
  • Version 2.1: 2019-12-25
    Changes: Author supporting evidence
  • Version 2.2: 2023-09-27
    Changes: Advisory, Data collection, Database references, Refinement description