2PPP

Crystal structure of E60Q mutant of FKBP12


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.94 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.203 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural coupling between FKBP12 and buried water.

Szep, S.Park, S.Boder, E.T.Van Duyne, G.D.Saven, J.G.

(2009) Proteins 74: 603-611

  • DOI: 10.1002/prot.22176
  • Primary Citation of Related Structures:  
    2PPP, 2PPO, 2PPN

  • PubMed Abstract: 
  • Globular proteins often contain structurally well-resolved internal water molecules. Previously, we reported results from a molecular dynamics study that suggested that buried water (Wat3) may play a role in modulating the structure of the FK506 binding ...

    Globular proteins often contain structurally well-resolved internal water molecules. Previously, we reported results from a molecular dynamics study that suggested that buried water (Wat3) may play a role in modulating the structure of the FK506 binding protein-12 (FKBP12) (Park and Saven, Proteins 2005; 60:450-463). In particular, simulations suggested that disrupting a hydrogen bond to Wat3 by mutating E60 to either A or Q would cause a structural perturbation involving the distant W59 side chain, which rotates to a new conformation in response to the mutation. This effectively remodels the ligand-binding pocket, as the side chain in the new conformation is likely to clash with bound FK506. To test whether the protein structure is in effect modulated by the binding of a buried water in the distance, we determined high-resolution (0.92-1.29 A) structures of wild-type FKBP12 and its two mutants (E60A, E60Q) by X-ray crystallography. The structures of mutant FKBP12 show that the ligand-binding pocket is indeed remodeled as predicted by the substitution at position 60, even though the water molecule does not directly interact with any of the amino acids of the binding pocket. Thus, these structures support the view that buried water molecules constitute an integral, noncovalent component of the protein structure. Additionally, this study provides an example in which predictions from molecular dynamics simulations are experimentally validated with atomic precision, thus showing that the structural features of protein-water interactions can be reliably modeled at a molecular level.


    Organizational Affiliation

    Department of Biochemistry and Biophysics, Howard Hughes Medical Institute, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
FK506-binding protein 1A A107Homo sapiensMutation(s): 1 
Gene Names: FKBP1AFKBP1FKBP12
EC: 5.2.1.8
Find proteins for P62942 (Homo sapiens)
Explore P62942 
Go to UniProtKB:  P62942
NIH Common Fund Data Resources
PHAROS:  P62942
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.94 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.203 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 28.602α = 90
b = 62.517β = 114.14
c = 32.248γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
CCP4model building
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing
ADSCdata collection

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-09-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2019-07-24
    Changes: Data collection, Refinement description