3NKE

High resolution structure of the C-terminal domain CRISP-associated protein Cas1 from Escherichia coli str. K-12


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A dual function of the CRISPR-Cas system in bacterial antivirus immunity and DNA repair.

Babu, M.Beloglazova, N.Flick, R.Graham, C.Skarina, T.Nocek, B.Gagarinova, A.Pogoutse, O.Brown, G.Binkowski, A.Phanse, S.Joachimiak, A.Koonin, E.V.Savchenko, A.Emili, A.Greenblatt, J.Edwards, A.M.Yakunin, A.F.

(2011) Mol Microbiol 79: 484-502

  • DOI: 10.1111/j.1365-2958.2010.07465.x
  • Primary Citation of Related Structures:  
    3NKD, 3NKE

  • PubMed Abstract: 
  • Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) and the associated proteins (Cas) comprise a system of adaptive immunity against viruses and plasmids in prokaryotes. Cas1 is a CRISPR-associated protein that is common to all CRISPR-containing prokaryotes but its function remains obscure ...

    Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) and the associated proteins (Cas) comprise a system of adaptive immunity against viruses and plasmids in prokaryotes. Cas1 is a CRISPR-associated protein that is common to all CRISPR-containing prokaryotes but its function remains obscure. Here we show that the purified Cas1 protein of Escherichia coli (YgbT) exhibits nuclease activity against single-stranded and branched DNAs including Holliday junctions, replication forks and 5'-flaps. The crystal structure of YgbT and site-directed mutagenesis have revealed the potential active site. Genome-wide screens show that YgbT physically and genetically interacts with key components of DNA repair systems, including recB, recC and ruvB. Consistent with these findings, the ygbT deletion strain showed increased sensitivity to DNA damage and impaired chromosomal segregation. Similar phenotypes were observed in strains with deletion of CRISPR clusters, suggesting that the function of YgbT in repair involves interaction with the CRISPRs. These results show that YgbT belongs to a novel, structurally distinct family of nucleases acting on branched DNAs and suggest that, in addition to antiviral immunity, at least some components of the CRISPR-Cas system have a function in DNA repair.


    Organizational Affiliation

    Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, M5G 1L6, Canada.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
protein ygbTA, B, C200Escherichia coli K-12Mutation(s): 0 
Gene Names: ygbTb2755JW2725cas1
EC: 3.1
Find proteins for Q46896 (Escherichia coli (strain K12))
Explore Q46896 
Go to UniProtKB:  Q46896
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.709α = 90
b = 90.047β = 90
c = 121.876γ = 90
Software Package:
Software NamePurpose
SBC-Collectdata collection
HKL-3000phasing
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: 2010-08-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2014-12-17
    Changes: Data collection