1P56

Duplication-extension of Helix A of T4 lysozyme


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Relocation or duplication of the helix A sequence of T4 lysozyme causes only modest changes in structure but can increase or decrease the rate of folding.

Sagermann, M.Baase, W.A.Mooers, B.H.Gay, L.Matthews, B.W.

(2004) Biochemistry 43: 1296-1301

  • DOI: 10.1021/bi035702q
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • In T4 lysozyme, helix A is located at the amino terminus of the sequence but is associated with the C-terminal domain in the folded structure. To investigate the implications of this arrangement for the folding of the protein, we first created a circ ...

    In T4 lysozyme, helix A is located at the amino terminus of the sequence but is associated with the C-terminal domain in the folded structure. To investigate the implications of this arrangement for the folding of the protein, we first created a circularly permuted variant with a new amino terminus at residue 12. In effect, this moves the sequence corresponding to helix A from the N- to the C-terminus of the molecule. The protein crystallized nonisomorphously with the wild type but has a very similar structure, showing that the unit consisting of helix A and the C-terminal domain can be reconstituted from a contiguous polypeptide chain. The protein is less stable than the wild type but folds slightly faster. We then produced a second variant in which the helix A sequence was appended at the C-terminus (as in the first variant), but was also restored at the N-terminus (as in the wild type). This variant has two helix A sequences, one at the N-terminus and the other at the C-terminus, each of which can compete for the same site in the folded protein. The crystal structure shows that it is the N-terminal sequence that folds in a manner similar to that of the wild type, whereas the copy at the C-terminus is forced to loop out. The stability of this protein is much closer to that of the wild type, but its rate of folding is significantly slower. The reduction in rate is attributed to the presence of the two identical sequence segments which compete for a single, mutually exclusive, site.


    Related Citations: 
    • Crystal structures of a T4-lysozyme duplication-extension mutant demonstrates that the highly conserved beta-sheet region has low intrinsic folding propensity
      Sagermann, M.,Matthews, B.W.
      (2002) J.Mol.Biol. 316: 931
    • Structure of bacteriophage T4 lysozyme refined at 1.7 A resolution
      Weaver, L.H.,Matthews, B.W.
      (1987) J.Mol.Biol. 193: 189
    • Structural characterization of an engineered tandem repeat contrasts the importance of context and sequence in protein folding
      Sagermann, M.,Baase, W.A.,Matthews, B.W.
      (1999) Proc.Natl.Acad.Sci.USA 96: 6078


    Organizational Affiliation

    Institute of Molecular Biology, Howard Hughes Medical Institute, and Department of Physics, 1229, University of Oregon, Eugene, Oregon 97403-1229, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (Lysozyme)
A
176Enterobacteria phage T4Mutations: C97A, C54T
Gene Names: E
EC: 3.2.1.17
Find proteins for P00720 (Enterobacteria phage T4)
Go to UniProtKB:  P00720
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.208 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 60.300α = 90.00
b = 60.300β = 90.00
c = 96.396γ = 120.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
TNTrefinement
CNSrefinement
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-05-04
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance