4NXP

Crystal Structure of Free T-cell Lymphoma Invasion and Metastasis-1 PDZ Domain Quadruple Mutant (QM)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.219 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Distinct Roles for Conformational Dynamics in Protein-Ligand Interactions.

Liu, X.Speckhard, D.C.Shepherd, T.R.Sun, Y.J.Hengel, S.R.Yu, L.Fowler, C.A.Gakhar, L.Fuentes, E.J.

(2016) Structure 24: 2053-2066

  • DOI: 10.1016/j.str.2016.08.019
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Conformational dynamics has an established role in enzyme catalysis, but its contribution to ligand binding and specificity is largely unexplored. Here we used the Tiam1 PDZ domain and an engineered variant (QM PDZ) with broadened specificity to inve ...

    Conformational dynamics has an established role in enzyme catalysis, but its contribution to ligand binding and specificity is largely unexplored. Here we used the Tiam1 PDZ domain and an engineered variant (QM PDZ) with broadened specificity to investigate the role of structure and conformational dynamics in molecular recognition. Crystal structures of the QM PDZ domain both free and bound to ligands showed structural features central to binding (enthalpy), while nuclear-magnetic-resonance-based methyl relaxation experiments and isothermal titration calorimetry revealed that conformational entropy contributes to affinity. In addition to motions relevant to thermodynamics, slower microsecond to millisecond switching was prevalent in the QM PDZ ligand-binding site consistent with a role in ligand specificity. Our data indicate that conformational dynamics plays distinct and fundamental roles in tuning the affinity (conformational entropy) and specificity (excited-state conformations) of molecular interactions. More broadly, our results have important implications for the evolution, regulation, and design of protein-ligand interactions.


    Organizational Affiliation

    Department of Biochemistry, University of Iowa, Iowa City, IA 52242-1109, USA; Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA 52242-1109, USA; Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242-1109, USA. Electronic address: ernesto-fuentes@uiowa.edu.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
T-lymphoma invasion and metastasis-inducing protein 1
A
94Homo sapiensMutation(s): 5 
Gene Names: TIAM1
Find proteins for Q13009 (Homo sapiens)
Go to UniProtKB:  Q13009
NIH Common Fund Data Resources
PHAROS  Q13009
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.219 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.843α = 90
b = 45.843β = 90
c = 71.362γ = 120
Software Package:
Software NamePurpose
StructureStudiodata collection
PHASERphasing
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-05-13
    Type: Initial release
  • Version 1.1: 2017-02-15
    Changes: Database references