1JKP

Testing the Water-Mediated HIN Recombinase DNA Recognition by Systematic Mutations


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.328 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.248 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Testing water-mediated DNA recognition by the Hin recombinase.

Chiu, T.K.Sohn, C.Dickerson, R.E.Johnson, R.C.

(2002) EMBO J 21: 801-814

  • DOI: 10.1093/emboj/21.4.801
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The Hin recombinase specifically recognizes its DNA-binding site by means of both major and minor groove interactions. A previous X-ray structure, together with new structures of the Hin DNA-binding domain bound to a recombination half-site that were ...

    The Hin recombinase specifically recognizes its DNA-binding site by means of both major and minor groove interactions. A previous X-ray structure, together with new structures of the Hin DNA-binding domain bound to a recombination half-site that were solved as part of the present study, have revealed that two ordered water molecules are present within the major groove interface. In this report, we test the importance of these waters directly by X-ray crystal structure analysis of complexes with four mutant DNA sequences. These structures, combined with their Hin-binding properties, provide strong support for the critical importance of one of the intermediate waters. A lesser but demonstrable role is ascribed to the second water molecule. The mutant structures also illustrate the prominent roles of thymine methyls both in stabilizing intermediate waters and in interfering with water or amino acid side chain interactions with DNA.


    Related Citations: 
    • How Hin Recombinase, FIS and Cations Bind DNA. Chapter 4. Water-Mediated Sequence-Specific Recognition by Hin Recombinase
      Chiu, T.K.
      (2001) Thesis --: 145
    • Hin Recombinase Bound to DNA: The Origin of Specificity in Major and Minor Groove Interactions
      Feng, J.A., Johnson, R.C., Dickerson, R.E.
      (1994) Science 263: 348

    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of California at Los Angeles, Los Angeles, CA 90095, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA-INVERTASE HIN
C
52N/AMutation(s): 0 
Find proteins for P03013 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Go to UniProtKB:  P03013
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*TP*GP*TP*TP*TP*TP*TP*GP*AP*GP*AP*AP*GP*A)-3'A14N/A
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*AP*TP*CP*TP*TP*CP*TP*CP*AP*AP*AP*AP*AP*C)-3'B14N/A
Small Molecules
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DNAKd :  2.049999952316284   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.328 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.248 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.362α = 90
b = 81.543β = 90
c = 45.39γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-02-22
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance