1HX7

SOLUTION STRUCTURE OF THE CATALYTIC DOMAIN OF GAMMA DELTA RESOLVASE


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 19 
  • Selection Criteria: lowest energy and agreement with experimental NOESY 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Solution structure of the catalytic domain of gammadelta resolvase. Implications for the mechanism of catalysis.

Pan, B.Maciejewski, M.W.Marintchev, A.Mullen, G.P.

(2001) J.Mol.Biol. 310: 1089-1107

  • DOI: 10.1006/jmbi.2001.4821
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The site-specific DNA recombinase, gammadelta resolvase, from Escherichia coli catalyzes recombination of res site-containing plasmid DNA to two catenated circular DNA products. The catalytic domain (residues 1-105), lacking a C-terminal dimerization ...

    The site-specific DNA recombinase, gammadelta resolvase, from Escherichia coli catalyzes recombination of res site-containing plasmid DNA to two catenated circular DNA products. The catalytic domain (residues 1-105), lacking a C-terminal dimerization interface, has been constructed and the NMR solution structure of the monomer determined. The RMSD of the NMR conformers for residues 2-92 excluding residues 37-45 and 64-73 is 0.41 A for backbone atoms and 0.88 A for all heavy atoms. The NMR solution structure of the monomeric catalytic domain (residues 1-105) was found to be formed by a four-stranded parallel beta-sheet surrounded by three helices. The catalytic domain (residues 1-105), deficient in the C-terminal dimerization domain, was monomeric at high salt concentration, but displayed unexpected dimerization at lower ionic strength. The unique solution dimerization interface at low ionic strength was mapped by NMR. With respect to previous crystal structures of the dimeric catalytic domain (residues 1-140), differences in the average conformation of active-site residues were found at loop 1 containing the catalytic S10 nucleophile, the beta1 strand containing R8, and at loop 3 containing D67, R68 and R71, which are required for catalysis. The active-site loops display high-frequency and conformational backbone dynamics and are less well defined than the secondary structures. In the solution structure, the D67 side-chain is proximal to the S10 side-chain making the D67 carboxylate group a candidate for activation of S10 through general base catalysis. Four conserved Arg residues can function in the activation of the phosphodiester for nucleophilic attack by the S10 hydroxyl group. A mechanism for covalent catalysis by this class of recombinases is proposed that may be related to dimer interface dissociation.


    Related Citations: 
    • 1H, 15N and 13C Resonance Assignments for the Catalytic Core of Gamma Delta Resolvase
      Pan, B.,Mullen, G.P.
      (1999) J.Biomol.NMR 13: 307


    Organizational Affiliation

    Department of Biochemistry, University of Connecticut Health Center, Farmington 06032, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TRANSPOSON GAMMA-DELTA RESOLVASE
A
105Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: tnpR
Find proteins for P03012 (Escherichia coli (strain K12))
Go to UniProtKB:  P03012
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 19 
  • Selection Criteria: lowest energy and agreement with experimental NOESY 
  • Olderado: 1HX7 Olderado

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2001-01-11 
  • Released Date: 2002-01-16 
  • Deposition Author(s): Pan, B., Mullen, G.P.

Revision History 

  • Version 1.0: 2002-01-16
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance