4XQK

ATP-dependent Type ISP restriction-modification enzyme LlaBIII bound to DNA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.221 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Translocation-coupled DNA cleavage by the Type ISP restriction-modification enzymes

Chand, M.K., Nirwan, N., Diffin, F.M., Aelst, K.V., Kulkarni, M., Pernstich, C., Szczelkun, M.D., Saikrishnan, K.

(2015) Nat Chem Biol 11: 870-877

  • DOI: https://doi.org/10.1038/nchembio.1926
  • Primary Citation of Related Structures:  
    4XQK

  • PubMed Abstract: 

    • Production of endonucleolytic double-strand DNA breaks requires separate strand cleavage events. Although catalytic mechanisms for simple, dimeric endonucleases are known, there are many complex nuclease machines that are poorly understood. Here we studied the single polypeptide Type ISP restriction-modification (RM) enzymes, which cleave random DNA between distant target sites when two enzymes collide after convergent ATP-driven translocation ...

    Production of endonucleolytic double-strand DNA breaks requires separate strand cleavage events. Although catalytic mechanisms for simple, dimeric endonucleases are known, there are many complex nuclease machines that are poorly understood. Here we studied the single polypeptide Type ISP restriction-modification (RM) enzymes, which cleave random DNA between distant target sites when two enzymes collide after convergent ATP-driven translocation. We report the 2.7-Å resolution X-ray crystal structure of a Type ISP enzyme-DNA complex, revealing that both the helicase-like ATPase and nuclease are located upstream of the direction of translocation, an observation inconsistent with simple nuclease-domain dimerization. Using single-molecule and biochemical techniques, we demonstrate that each ATPase remodels its DNA-protein complex and translocates along DNA without looping it, leading to a collision complex in which the nuclease domains are distal. Sequencing of the products of single cleavage events suggests a previously undescribed endonuclease model, where multiple, stochastic strand-nicking events combine to produce DNA scission.

    Organizational Affiliation: 

    Division of Biology, Indian Institute of Science Education and Research, Pune, India.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
LlaBIII
A, B
1,578Lactococcus cremorisMutation(s): 0 
UniProt
Find proteins for A0A0M3KL05 (Lactococcus lactis subsp. cremoris)
Explore A0A0M3KL05 
Go to UniProtKB:  A0A0M3KL05
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0M3KL05
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (28-MER)
C, E
28synthetic construct
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsLengthOrganismImage
DNA (28-MER)
D, F
28synthetic construct
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K
Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
I [auth B]		POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.221 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.88α = 103.3
b = 112.66β = 90.88
c = 146.21γ = 105.79
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Wellcome Trust-DBT India AllianceIndia500048-Z-09-Z

Revision History  (Full details and data files)

  • Version 1.0: 2015-09-16
    Type: Initial release
  • Version 1.1: 2015-09-23
    Changes: Data collection
  • Version 1.2: 2015-11-04
    Changes: Database references
  • Version 1.3: 2020-02-05
    Changes: Data collection, Derived calculations, Source and taxonomy