3PKZ

Structural basis for catalytic activation of a serine recombinase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis for catalytic activation of a serine recombinase.

Keenholtz, R.A.Rowland, S.J.Boocock, M.R.Stark, W.M.Rice, P.A.

(2011) Structure 19: 799-809

  • DOI: 10.1016/j.str.2011.03.017
  • Primary Citation of Related Structures:  
    3PKZ

  • PubMed Abstract: 
  • Sin resolvase is a site-specific serine recombinase that is normally controlled by a complex regulatory mechanism. A single mutation, Q115R, allows the enzyme to bypass the entire regulatory apparatus, such that no accessory proteins or DNA sites are required ...

    Sin resolvase is a site-specific serine recombinase that is normally controlled by a complex regulatory mechanism. A single mutation, Q115R, allows the enzyme to bypass the entire regulatory apparatus, such that no accessory proteins or DNA sites are required. Here, we present a 1.86 Å crystal structure of the Sin Q115R catalytic domain, in a tetrameric arrangement stabilized by an interaction between Arg115 residues on neighboring subunits. The subunits have undergone significant conformational changes from the inactive dimeric state previously reported. The structure provides a new high-resolution view of a serine recombinase active site that is apparently fully assembled, suggesting roles for the conserved active site residues. The structure also suggests how the dimer-tetramer transition is coupled to assembly of the active site. The tetramer is captured in a different rotational substate than that seen in previous hyperactive serine recombinase structures, and unbroken crossover site DNA can be readily modeled into its active sites.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Recombinase Sin
A, B, C, D, E, F, G, H
A, B, C, D, E, F, G, H, I, J, K, L
124Staphylococcus aureusMutation(s): 2 
Gene Names: sinSAP013A_018SAP095A_006SAP096A_020bin3
Find proteins for P20384 (Staphylococcus aureus)
Explore P20384 
Go to UniProtKB:  P20384
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth I] , BA [auth I] , CA [auth I] , FA [auth J] , GA [auth K] , IA [auth L] , JA [auth L] , M [auth A] , 
AA [auth I],  BA [auth I],  CA [auth I],  FA [auth J],  GA [auth K],  IA [auth L],  JA [auth L],  M [auth A],  N [auth A],  O [auth B],  P [auth C],  Q [auth C],  R [auth D],  S [auth D],  T [auth E],  U [auth E],  V [auth F],  W [auth G],  X [auth H],  Y [auth H]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
DA [auth I], HA [auth K]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
EA [auth I], Z [auth H]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.208α = 90
b = 128.208β = 90
c = 182.015γ = 120
Software Package:
Software NamePurpose
HKL-3000data collection
SOLVEphasing
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-06-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-03-28
    Changes: Database references