6NJX

C-terminal region of the Xanthomonas campestris pv. campestris OLD protein phased with mercury

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 

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This is version 1.2 of the entry. See complete history. 


Literature

Structural characterization of Class 2 OLD family nucleases supports a two-metal catalysis mechanism for cleavage.

Schiltz, C.J., Lee, A., Partlow, E.A., Hosford, C.J., Chappie, J.S.

(2019) Nucleic Acids Res 47: 9448-9463

  • DOI: 10.1093/nar/gkz703
  • Primary Citation of Related Structures:  
    6NJV, 6NJW, 6NJX, 6NK8

  • PubMed Abstract: 

    • Overcoming lysogenization defect (OLD) proteins constitute a family of uncharacterized nucleases present in bacteria, archaea, and some viruses. These enzymes contain an N-terminal ATPase domain and a C-terminal Toprim domain common amongst replication, recombination, and repair proteins ...

    Overcoming lysogenization defect (OLD) proteins constitute a family of uncharacterized nucleases present in bacteria, archaea, and some viruses. These enzymes contain an N-terminal ATPase domain and a C-terminal Toprim domain common amongst replication, recombination, and repair proteins. The in vivo activities of OLD proteins remain poorly understood and no definitive structural information exists. Here we identify and define two classes of OLD proteins based on differences in gene neighborhood and amino acid sequence conservation and present the crystal structures of the catalytic C-terminal regions from the Burkholderia pseudomallei and Xanthamonas campestris p.v. campestris Class 2 OLD proteins at 2.24 Å and 1.86 Å resolution respectively. The structures reveal a two-domain architecture containing a Toprim domain with altered architecture and a unique helical domain. Conserved side chains contributed by both domains coordinate two bound magnesium ions in the active site of B. pseudomallei OLD in a geometry that supports a two-metal catalysis mechanism for cleavage. The spatial organization of these domains additionally suggests a novel mode of DNA binding that is distinct from other Toprim containing proteins. Together, these findings define the fundamental structural properties of the OLD family catalytic core and the underlying mechanism controlling nuclease activity.

    Organizational Affiliation: 

    Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Xcc_ctr_HgA230Xanthomonas campestris pv. campestris str. B100Mutation(s): 0 
Gene Names: XCCB100_2436
UniProt
Find proteins for B0RTN2 (Xanthomonas campestris pv. campestris (strain B100))
Explore B0RTN2 
Go to UniProtKB:  B0RTN2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB0RTN2
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.189α = 90
b = 65.189β = 90
c = 63.799γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
AutoSolphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-08-07
    Type: Initial release
  • Version 1.1: 2019-08-21
    Changes: Data collection, Database references
  • Version 1.2: 2019-10-09
    Changes: Data collection, Database references