3S4L | pdb_00003s4l

The CRISPR-associated Cas3 HD domain protein MJ0384 from Methanocaldococcus jannaschii


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.272 (Depositor), 0.267 (DCC) 
  • R-Value Work: 
    0.234 (Depositor), 0.228 (DCC) 
  • R-Value Observed: 
    0.235 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history

Literature

Structure and activity of the Cas3 HD nuclease MJ0384, an effector enzyme of the CRISPR interference.

Beloglazova, N.Petit, P.Flick, R.Brown, G.Savchenko, A.Yakunin, A.F.

(2011) EMBO J 30: 4616-4627

  • DOI: https://doi.org/10.1038/emboj.2011.377
  • Primary Citation Related Structures: 
    3S4L

  • PubMed Abstract: 

    Clustered regularly interspaced short palindromic repeats (CRISPRs) and Cas proteins represent an adaptive microbial immunity system against viruses and plasmids. Cas3 proteins have been proposed to play a key role in the CRISPR mechanism through the direct cleavage of invasive DNA. Here, we show that the Cas3 HD domain protein MJ0384 from Methanocaldococcus jannaschii cleaves endonucleolytically and exonucleolytically (3'-5') single-stranded DNAs and RNAs, as well as 3'-flaps, splayed arms, and R-loops. The degradation of branched DNA substrates by MJ0384 is stimulated by the Cas3 helicase MJ0383 and ATP. The crystal structure of MJ0384 revealed the active site with two bound metal cations and together with site-directed mutagenesis suggested a catalytic mechanism. Our studies suggest that the Cas3 HD nucleases working together with the Cas3 helicases can completely degrade invasive DNAs through the combination of endo- and exonuclease activities.


  • Organizational Affiliation
    • Department of Chemical Engineering and Applied Chemistry, Banting and Best Department of Medical Research, University of Toronto, Ontario, Canada.

Macromolecule Content 

  • Total Structure Weight: 28.53 kDa 
  • Atom Count: 1,615 
  • Modeled Residue Count: 197 
  • Deposited Residue Count: 244 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
CAS3 Metal dependent phosphohydrolase244Methanocaldococcus jannaschii DSM 2661Mutation(s): 0 
Gene Names: MJ0384Y384_METJA
EC: 3.1
UniProt
Find proteins for Q57829 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
Explore Q57829 
Go to UniProtKB:  Q57829
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ57829
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.272 (Depositor), 0.267 (DCC) 
  • R-Value Work:  0.234 (Depositor), 0.228 (DCC) 
  • R-Value Observed: 0.235 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.073α = 90
b = 59.073β = 90
c = 162.879γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
SHELXDphasing
PHENIXrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-06-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-10-05
    Changes: Structure summary
  • Version 1.3: 2020-02-12
    Changes: Database references
  • Version 1.4: 2024-02-28
    Changes: Data collection, Database references, Derived calculations