6QZK

Structure of Clostridium butyricum Argonaute bound to a guide DNA (5' deoxycytidine) and a 19-mer target DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.55 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.250 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

DNA-guided DNA cleavage at moderate temperatures by Clostridium butyricum Argonaute.

Hegge, J.W.Swarts, D.C.Chandradoss, S.D.Cui, T.J.Kneppers, J.Jinek, M.Joo, C.van der Oost, J.

(2019) Nucleic Acids Res 47: 5809-5821

  • DOI: https://doi.org/10.1093/nar/gkz306
  • Primary Citation of Related Structures:  
    6QZK

  • PubMed Abstract: 

    Prokaryotic Argonaute proteins (pAgos) constitute a diverse group of endonucleases of which some mediate host defense by utilizing small interfering DNA guides (siDNA) to cleave complementary invading DNA. This activity can be repurposed for programmable DNA cleavage. However, currently characterized DNA-cleaving pAgos require elevated temperatures (≥65°C) for their activity, making them less suitable for applications that require moderate temperatures, such as genome editing. Here, we report the functional and structural characterization of the siDNA-guided DNA-targeting pAgo from the mesophilic bacterium Clostridium butyricum (CbAgo). CbAgo displays a preference for siDNAs that have a deoxyadenosine at the 5'-end and thymidines at nucleotides 2-4. Furthermore, CbAgo mediates DNA-guided DNA cleavage of AT-rich double stranded DNA at moderate temperatures (37°C). This study demonstrates that certain pAgos are capable of programmable DNA cleavage at moderate temperatures and thereby expands the scope of the potential pAgo-based applications.


  • Organizational Affiliation

    Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, 6708 WE Wageningen, The Netherlands.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Clostridium butyricum Argonaute748Clostridium butyricumMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
siDNA guide (5'-D(P*CP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*TP*AP*GP*T)-3')21synthetic construct
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA target (5'-D(T*AP*TP*AP*CP*AP*AP*CP*CP*TP*AP*CP*TP*AP*CP*CP*TP*CP*T)-3')19synthetic construct
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.55 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.250 
  • Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 181.45α = 90
b = 181.45β = 90
c = 142.99γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Molecular Biology OrganizationSwitzerlandALTF 179-2015
European Molecular Biology OrganizationSwitzerlandaALTF 509-2017
Swiss National Science FoundationSwitzerlandSNSF 31003A_149393
Netherlands Organisation for Scientific ResearchNetherlands711013002
Netherlands Organisation for Scientific ResearchNetherlands714.015.001
Netherlands Organisation for Scientific ResearchNetherlands016.Veni.192.072

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-24
    Type: Initial release
  • Version 1.1: 2019-05-22
    Changes: Data collection, Database references
  • Version 1.2: 2019-06-26
    Changes: Data collection, Database references
  • Version 1.3: 2024-01-24
    Changes: Data collection, Database references, Derived calculations, Refinement description