6P0G

N-terminal domain of Thermococcus Gammatolerans McrB bound to m5C DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.238 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The structure of the Thermococcus gammatolerans McrB N-terminal domain reveals a new mode of substrate recognition and specificity among McrB homologs.

Hosford, C.J.Bui, A.Q.Chappie, J.S.

(2019) J.Biol.Chem. --: --

  • DOI: 10.1074/jbc.RA119.010188
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • McrBC is a two-component, modification-dependent restriction system that cleaves foreign DNA containing methylated cytosines. Previous crystallographic studies have shown that Escherichia coli McrB uses a base-flipping mechanism to recognize these mo ...

    McrBC is a two-component, modification-dependent restriction system that cleaves foreign DNA containing methylated cytosines. Previous crystallographic studies have shown that Escherichia coli McrB uses a base-flipping mechanism to recognize these modified substrates with high affinity. The sidechains stabilizing both the flipped base and the distorted duplex are poorly conserved among McrB homologs, suggesting that other mechanisms may exist for binding modified DNA. Here we present the structures of the Thermococcus gammatolerans McrB DNA binding domain (Tg∆185) both alone and in complex with a methylated DNA substrate at 1.68 Å and 2.27 Å resolution respectively. The structures reveal that Tg∆185 consists of a YT521-B homology (YTH) domain, which is commonly found in eukaryotic proteins that bind methylated RNA and is structurally unrelated to the E. coli McrB DNA binding domain. Structural superposition and co-crystallization further show that Tg∆185 shares a conserved aromatic cage with other YTH domains, which forms the binding pocket for a flipped-out base. Mutational analysis of this aromatic cage supports its role in conferring specificity for the methylated adenines while an extended basic surface present in Tg∆185 facilitates its preferential binding to duplex DNA rather than RNA. Together these findings establish a new binding mode and specificity among McrB homologs and expand the biological roles of YTH domains.


    Organizational Affiliation

    Molecular Medicine, Cornell University, United States.,Cornell University, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GTPase subunit of restriction endonuclease
A
185Thermococcus gammatolerans (strain DSM 15229 / JCM 11827 / EJ3)Mutation(s): 0 
Find proteins for C5A3Z3 (Thermococcus gammatolerans (strain DSM 15229 / JCM 11827 / EJ3))
Go to UniProtKB:  C5A3Z3
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(P*TP*AP*CP*CP*GP*G)-3')B6synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(P*AP*CP*CP*GP*GP*T)-3')C6synthetic construct
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.238 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 41.166α = 90.00
b = 57.304β = 90.00
c = 107.507γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
Aimlessdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM120242

Revision History 

  • Version 1.0: 2019-12-18
    Type: Initial release
  • Version 1.1: 2019-12-25
    Type: Database references