2FCO

Crystal Structure of Bacillus stearothermophilus PrfA-Holliday Junction Resolvase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.214 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure, flexibility, and mechanism of the Bacillus stearothermophilus RecU Holliday junction resolvase.

Kelly, S.J.Li, J.Setlow, P.Jedrzejas, M.J.

(2007) Proteins 68: 961-971

  • DOI: 10.1002/prot.21418
  • Primary Citation of Related Structures:  
    2FCO

  • PubMed Abstract: 
  • Here we report a high resolution structure of RecU-Holliday junction resolvase from Bacillus stearothermophilus. The functional unit of RecU is a homodimer that contains a "mushroom" like structure with a rigid cap and two highly flexible loops extending outwards ...

    Here we report a high resolution structure of RecU-Holliday junction resolvase from Bacillus stearothermophilus. The functional unit of RecU is a homodimer that contains a "mushroom" like structure with a rigid cap and two highly flexible loops extending outwards. These loops appear to be highly flexible/dynamic, and presumably are directly involved in DNA binding and holding it for catalysis. Structural modifications of both the protein and DNA upon their interaction are essential for catalysis. An Mg2+ ion is present in each of the two active sites in this homodimeric enzyme, and two water molecules are coordinated with each Mg2+ ion. Our data are consistent with one of these water molecules acting as a nucleophile and the other as a general acid. The identities of the general base and general acid involved in catalysis and the Lewis acid that stabilizes the pentacovalent transition state phosphate ion are proposed. A model for the RecU-Holliday junction DNA complex is also proposed and discussed in the context of DNA binding and cleavage.


    Organizational Affiliation

    Children's Hospital Oakland Research Institute, Oakland, CA 94609, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
recombination protein U (penicillin-binding protein related factor A)A, B200Geobacillus kaustophilus HTA426Mutation(s): 0 
Gene Names: RecU/PrfArecUGK2167
EC: 3.1.22.4
Find proteins for Q5KXY4 (Geobacillus kaustophilus (strain HTA426))
Explore Q5KXY4 
Go to UniProtKB:  Q5KXY4
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download Ideal Coordinates CCD File 
E [auth B], F [auth B]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth A], D [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.214 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.886α = 90
b = 96.886β = 90
c = 114.539γ = 120
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-11-21
    Type: Initial release
  • Version 1.1: 2007-11-14
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance