1JJ8

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.3 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
  • Primary Citation of Related Structures:  1IJW, 1JJ6, 1JKO, 1JKP, 1JKQ, 1JKR

  • 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: 
    • 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
    • How Hin Recombinase, FIS and Cations Bind DNA. Chapter 4. Water-Mediated Sequence-Specific Recognition by Hin Recombinase.
      Chiu, T.K.
      (2001) Thesis --: 145


    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
52Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)Gene Names: hin
Find proteins for P03013 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Go to UniProtKB:  P03013
Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*TP*GP*(5IT)P*TP*TP*TP*TP*GP*AP*TP*AP*AP*GP*A)-3'A14N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*AP*TP*CP*TP*TP*AP*TP*CP*AP*AP*AP*AP*AP*C)-3'B14N/A
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
5IU
Query on 5IU
A
DNA LINKINGC9 H12 I N2 O8 PDU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.213 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 66.328α = 90.00
b = 68.693β = 90.00
c = 62.136γ = 90.00
Software Package:
Software NamePurpose
SOLVEphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-02-22
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2015-02-04
    Type: Database references, Other