8Q5O

N-terminal domain of restriction endonuclease Eco15I with tetra-methylated target DNA.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.264 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural analysis of the BisI family of modification dependent restriction endonucleases.

Szafran, K.Rafalski, D.Skowronek, K.Wojciechowski, M.Kazrani, A.A.Gilski, M.Xu, S.Y.Bochtler, M.

(2024) Nucleic Acids Res 52: 9103-9118

  • DOI: https://doi.org/10.1093/nar/gkae634
  • Primary Citation of Related Structures:  
    8Q5M, 8Q5N, 8Q5O, 8RPX

  • PubMed Abstract: 

    The BisI family of restriction endonucleases is unique in requiring multiple methylated or hydroxymethylated cytosine residues within a short recognition sequence (GCNGC), and in cleaving directly within this sequence, rather than at a distance. Here, we report that the number of modified cytosines that are required for cleavage can be tuned by the salt concentration. We present crystal structures of two members of the BisI family, NhoI and Eco15I_Ntd (N-terminal domain of Eco15I), in the absence of DNA and in specific complexes with tetra-methylated GCNGC target DNA. The structures show that NhoI and Eco15I_Ntd sense modified cytosine bases in the context of double-stranded DNA (dsDNA) without base flipping. In the co-crystal structures of NhoI and Eco15I_Ntd with DNA, the internal methyl groups (G5mCNGC) interact with the side chains of an (H/R)(V/I/T/M) di-amino acid motif near the C-terminus of the distal enzyme subunit and arginine residue from the proximal subunit. The external methyl groups (GCNG5mC) interact with the proximal enzyme subunit, mostly through main chain contacts. Surface plasmon resonance analysis for Eco15I_Ntd shows that the internal and external methyl binding pockets contribute about equally to sensing of cytosine methyl groups.


  • Organizational Affiliation

    International Institute of Molecular and Cell Biology, Warsaw, Poland.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Restriction endonuclease (Eco15I)
A, B
174Escherichia coliMutation(s): 0 
Gene Names: GIB53_21535IT029_004930J5U05_004825
UniProt
Find proteins for A0A0L6ZWS4 (Escherichia coli)
Explore A0A0L6ZWS4 
Go to UniProtKB:  A0A0L6ZWS4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0L6ZWS4
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*CP*TP*GP*(5CM)P*TP*GP*(5CM)P*TP*C)-3')9synthetic construct
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(*GP*AP*GP*(5CM)P*AP*GP*(5CM)P*AP*G)-3')9synthetic construct
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.264 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.995α = 90
b = 95.995β = 90
c = 96.307γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other government--

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-17
    Type: Initial release
  • Version 1.1: 2024-08-07
    Changes: Database references
  • Version 1.2: 2024-09-04
    Changes: Database references