1GDR

MODEL FOR A DNA MEDIATED SYNAPTIC COMPLEX SUGGESTED BY CRYSTAL PACKING OF GAMMA DELTA RESOLVASE SUBUNITS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Work: 0.310 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Model for a DNA-mediated synaptic complex suggested by crystal packing of gamma delta resolvase subunits.

Rice, P.A.Steitz, T.A.

(1994) EMBO J. 13: 1514-1524


  • PubMed Abstract: 
  • The packing arrangement of the 12 subunits of intact gamma delta resolvase in the unit cell of a hexagonal crystal form suggests a model for site-specific recombination that involves a DNA-mediated synaptic intermediate. The crystal structure has bee ...

    The packing arrangement of the 12 subunits of intact gamma delta resolvase in the unit cell of a hexagonal crystal form suggests a model for site-specific recombination that involves a DNA-mediated synaptic intermediate. The crystal structure has been determined by molecular replacement and partially refined at 2.8/3.5 A resolution. Although the small DNA-binding domain is disordered in these crystals, packing considerations show that only a small region of space in the crystal could accommodate a domain of its size. A family of related models for a synaptic complex between two DNA duplexes and 12 monomers that are arranged as situated in the crystal is consistent with the known topology of the complex and the distances between the three resolvase dimer-binding sites per DNA; further, these models place the two DNA recombination sites in contact with each other between two resolvase dimers, implying that strand exchange is accomplished through direct DNA-DNA interaction. A major role postulated, then, for the resolvase protein assembly is to stabilize a res DNA structure that is close to the topological transition state of the reaction.


    Related Citations: 
    • Cleavage of the Site-Specific Recombination Protein Gd Resolvase: The Smaller of Two Fragments Binds DNA Specifically
      Abdel-Muguid, S.S.,Grindley, N.D.F.,Templeton, N.S.,Steitz, T.A.
      (1984) Proc.Natl.Acad.Sci.USA 81: 2001
    • The Crystal Structure of the Catalytic Domain of the Site Specific Recombination Enzyme Gd Resolvase at 2.7 Resolution
      Sanderson, M.R.,Freemont, P.S.,Rice, P.A.,Goldman, A.,Hatfull, G.F.,Grindley, N.D.F.
      (1990) Cell 63: 1323
    • Preliminary X-Ray Diffraction Studies of the Putative Catalytic Domain of Gd Resolvase from Escherichia Coli
      Abdel-Meguid, S.S.,Murthy, H.M.K.,Steitz, T.A.
      (1986) J.Biol.Chem. 261: 15934
    • Crystallization of Resolvase, a Repressor that Also Catalyzes Site-Specific DNA Recombination
      Weber, P.C.,Ollis, D.L.,Bebrin, W.R.,Abdel-Meguid, S.S.,Steitz, T.A.
      (1982) J.Mol.Biol. 157: 689


    Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Yale University, New Haven, CT.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GAMMA DELTA-RESOLVASE
A
140Escherichia coli (strain K12)Gene Names: tnpR
Find proteins for P03012 (Escherichia coli (strain K12))
Go to UniProtKB:  P03012
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Work: 0.310 
  • Space Group: P 64 2 2
Unit Cell:
Length (Å)Angle (°)
a = 60.200α = 90.00
b = 60.200β = 90.00
c = 170.100γ = 120.00
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORphasing
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-04-30
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance