Crystal structure of Cas1 from Pectobacterium atrosepticum

Experimental Data Snapshot

  • Resolution: 2.70 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.188 

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Structural plasticity and in vivo activity of Cas1 from the type I-F CRISPR-Cas system.

Wilkinson, M.E.Nakatani, Y.Staals, R.H.Kieper, S.N.Opel-Reading, H.K.McKenzie, R.E.Fineran, P.C.Krause, K.L.

(2016) Biochem J 473: 1063-1072

  • DOI: https://doi.org/10.1042/BCJ20160078
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    CRISPR-Cas systems are adaptive immune systems in prokaryotes that provide protection against viruses and other foreign DNA. In the adaptation stage, foreign DNA is integrated into CRISPR (clustered regularly interspaced short palindromic repeat) arrays as new spacers. These spacers are used in the interference stage to guide effector CRISPR associated (Cas) protein(s) to target complementary foreign invading DNA. Cas1 is the integrase enzyme that is central to the catalysis of spacer integration. There are many diverse types of CRISPR-Cas systems, including type I-F systems, which are typified by a unique Cas1-Cas2-3 adaptation complex. In the present study we characterize the Cas1 protein of the potato phytopathogen Pectobacterium atrosepticum, an important model organism for understanding spacer acquisition in type I-F CRISPR-Cas systems. We demonstrate by mutagenesis that Cas1 is essential for adaptation in vivo and requires a conserved aspartic acid residue. By X-ray crystallography, we show that although P. atrosepticum Cas1 adopts a fold conserved among other Cas1 proteins, it possesses remarkable asymmetry as a result of structural plasticity. In particular, we resolve for the first time a flexible, asymmetric loop that may be unique to type I-F Cas1 proteins, and we discuss the implications of these structural features for DNA binding and enzymatic activity.

  • Organizational Affiliation

    Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand peter.fineran@otago.ac.nz kurt.krause@otago.ac.nz.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CRISPR-associated endonuclease Cas1
A, B, C, D, E
A, B, C, D, E, F
338Pectobacterium atrosepticum SCRI1043Mutation(s): 0 
Gene Names: cas1ECA3679
EC: 3.1
Find proteins for Q6D0X0 (Pectobacterium atrosepticum (strain SCRI 1043 / ATCC BAA-672))
Explore Q6D0X0 
Go to UniProtKB:  Q6D0X0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6D0X0
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.70 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.188 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 261.359α = 90
b = 164.065β = 90.09
c = 78.685γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
University of OtagoNew Zealand--
Royal Society of New ZealandNew Zealand--
Otago School of Medical SciencesNew Zealand--
Health Research Council (HRC)New Zealand--
Maurice Wilkins CentreNew Zealand--

Revision History  (Full details and data files)

  • Version 1.0: 2016-03-16
    Type: Initial release
  • Version 1.1: 2016-04-20
    Changes: Database references
  • Version 1.2: 2017-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2020-01-01
    Changes: Author supporting evidence