6QZK

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

• PDB DOI:  https://doi.org/10.2210/pdb6QZK/pdb
• NAKB: 6QZK

• Classification: HYDROLASE
• Organism(s): Clostridium butyricum, synthetic construct
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2019-03-11 Released: 2019-04-24 
• Deposition Author(s): Swarts, D.C., Jinek, M., Hegge, J.W., Van der Oost, J.
• Funding Organization(s): European Molecular Biology Organization, Swiss National Science Foundation, Netherlands Organisation for Scientific Research

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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 

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

• PubMed: 31069393 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 98.34 kDa 
• Atom Count: 6,749 
• Modelled Residue Count: 781 
• Deposited Residue Count: 788 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Clostridium butyricum Argonaute	A	748	Clostridium butyricum	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Length	Organism	Image
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')	B	21	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA target (5'-D(T*AP*TP*AP*CP*AP*AP*CP*CP*TP*AP*CP*TP*AP*CP*CP*TP*CP*T)-3')	C	19	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMT	E [auth A], F [auth A], G [auth B], H [auth B], I [auth B]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
MG	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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 = 181.45	α = 90
b = 181.45	β = 90
c = 142.99	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
AutoPROC	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-04-24 
Deposition Author(s): Swarts, D.C., Jinek, M., Hegge, J.W., Van der Oost, J.

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Funding Organization	Location	Grant Number
European Molecular Biology Organization	Switzerland	ALTF 179-2015
European Molecular Biology Organization	Switzerland	aALTF 509-2017
Swiss National Science Foundation	Switzerland	SNSF 31003A_149393
Netherlands Organisation for Scientific Research	Netherlands	711013002
Netherlands Organisation for Scientific Research	Netherlands	714.015.001
Netherlands Organisation for Scientific Research	Netherlands	016.Veni.192.072

Revision History  

• 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