220L

GENERATING LIGAND BINDING SITES IN T4 LYSOZYME USING DEFICIENCY-CREATING SUBSTITUTIONS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Work: 0.149 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Generation of ligand binding sites in T4 lysozyme by deficiency-creating substitutions.

Baldwin, E.Baase, W.A.Zhang, X.Feher, V.Matthews, B.W.

(1998) J Mol Biol 277: 467-485

  • DOI: 10.1006/jmbi.1997.1606
  • Primary Citation of Related Structures:  
    220L, 222L, 223L, 225L, 226L, 227L, 228L, 229L, 252L

  • PubMed Abstract: 
  • Several variants of T4 lysozyme have been identified that sequester small organic ligands in cavities or clefts. To evaluate potential binding sites for non-polar molecules, we screened a number of hydrophobic large-to-small mutants for stabilization in the presence of benzene ...

    Several variants of T4 lysozyme have been identified that sequester small organic ligands in cavities or clefts. To evaluate potential binding sites for non-polar molecules, we screened a number of hydrophobic large-to-small mutants for stabilization in the presence of benzene. In addition to Leu99-->Ala, binding was indicated for at least five other mutants. Variants Met102-->Ala and Leu133-->Gly, and a crevice mutant, Phe104-->Ala, were further characterized using X-ray crystallography and thermal denaturation. As predicted from the shape of the cavity in the benzene complex, mutant Leu133-->Gly also bound p-xylene. We attempted to enlarge the cavity of the Met102-->Ala mutant into a deep crevice through an additional substitution, but the double mutant failed to bind ligands because an adjacent helix rearranged into a non-helical structure, apparently due to the loss of packing interactions. In general, the protein structure contracted slightly to reduce the volume of the void created by truncating substitutions and expanded upon binding the non-polar ligand, with shifts similar to those resulting from the mutations.A polar molecule binding site was also created by truncating Arg95 to alanine. This creates a highly complementary buried polar environment that can be utilized as a specific "receptor" for a guanidinium ion. Our results suggest that creating a deficiency through truncating mutations of buried residues generates "binding potential" for ligands with characteristics similar to the deleted side-chain. Analysis of complex and apo crystal structures of binding and non-binding mutants suggests that ligand size and shape as well as protein flexibility and complementarity are all determinants of binding. Binding at non-polar sites is governed by hydrophobicity and steric interactions and is relatively permissive. Binding at a polar site is more restrictive and requires extensive complementarity between the ligand and the site.


    Related Citations: 
    • A Cavity-Containing Mutant of T4 Lysozyme is Stabilized by Buried Benzene
      Eriksson, A.E., Baase, W.A., Wozniak, J.A., Matthews, B.W.
      (1992) Nature 355: 371
    • Expression and Nitrogen-15 Labeling of Proteins for Proton and Nitrogen-15 Nuclear Magnetic Resonance
      Muchmore, D.C., Mcintosh, L.P., Russell, C.B., Anderson, D.E., Dahlquist, F.W.
      (1989) Methods Enzymol 177: 44
    • Structure of Bacteriophage T4 Lysozyme Refined at 1.7 A Resolution
      Weaver, L.H., Matthews, B.W.
      (1987) J Mol Biol 193: 189

    Organizational Affiliation

    Howard Hughes Medical Institute and Department of Physics, University of Oregon, Eugene, OR 97403, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
T4 LYSOZYMEA164Escherichia virus T4Mutation(s): 3 
Gene Names: GENE EE
EC: 3.2.1.17
UniProt
Find proteins for P00720 (Enterobacteria phage T4)
Explore P00720 
Go to UniProtKB:  P00720
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BME
Query on BME

Download Ideal Coordinates CCD File 
D [auth A], E [auth A]BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
 Ligand Interaction
BNZ
Query on BNZ

Download Ideal Coordinates CCD File 
F [auth A]BENZENE
C6 H6
UHOVQNZJYSORNB-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
B [auth A], C [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
BNZ PDBBind:  220L Kd: 4.00e+5 (nM) from 1 assay(s)
Binding MOAD:  220L Kd: 4.00e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Work: 0.149 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.9α = 90
b = 60.9β = 90
c = 97.2γ = 120
Software Package:
Software NamePurpose
TNTrefinement
SDMSdata reduction
SDMSdata scaling
TNTphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-03-18
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance