4NXR

Crystal Structure of T-cell Lymphoma Invasion and Metastasis-1 PDZ Domain Quadruple Mutant (QM) in Complex With Neurexin-1 Peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.147 

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
  • Primary Citation of Related Structures:  4NXP, 4NXQ

  • 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 bindingĀ (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; Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242-1109, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
T-lymphoma invasion and metastasis-inducing protein 1
A
94Homo sapiensGene Names: TIAM1
Find proteins for Q13009 (Homo sapiens)
Go to Gene View: TIAM1
Go to UniProtKB:  Q13009
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Neurexin-2-beta Peptide
B
8Homo sapiensGene Names: NRXN2
Find proteins for P58401 (Homo sapiens)
Go to Gene View: NRXN2
Go to UniProtKB:  P58401
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download SDF File 
Download CCD File 
A
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
ANS
Query on ANS

Download SDF File 
Download CCD File 
B
5-(DIMETHYLAMINO)-1-NAPHTHALENESULFONIC ACID(DANSYL ACID)
DANSYL ACID
C12 H13 N O3 S
BBEQQKBWUHCIOU-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.147 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 26.358α = 90.00
b = 50.323β = 90.00
c = 61.942γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
StructureStudiodata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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