1YF3

T4Dam in Complex with AdoHcy and 13-mer Oligonucleotide Making Non- and Semi-specific (~1/4) Contact


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Transition from Nonspecific to Specific DNA Interactions along the Substrate-Recognition Pathway of Dam Methyltransferase.

Horton, J.R.Liebert, K.Hattman, S.Jeltsch, A.Cheng, X.

(2005) Cell 121: 349-361

  • DOI: 10.1016/j.cell.2005.02.021
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • DNA methyltransferases methylate target bases within specific nucleotide sequences. Three structures are described for bacteriophage T4 DNA-adenine methyltransferase (T4Dam) in ternary complexes with partially and fully specific DNA and a methyl-dono ...

    DNA methyltransferases methylate target bases within specific nucleotide sequences. Three structures are described for bacteriophage T4 DNA-adenine methyltransferase (T4Dam) in ternary complexes with partially and fully specific DNA and a methyl-donor analog. We also report the effects of substitutions in the related Escherichia coli DNA methyltransferase (EcoDam), altering residues corresponding to those involved in specific interaction with the canonical GATC target sequence in T4Dam. We have identified two types of protein-DNA interactions: discriminatory contacts, which stabilize the transition state and accelerate methylation of the cognate site, and antidiscriminatory contacts, which do not significantly affect methylation of the cognate site but disfavor activity at noncognate sites. These structures illustrate the transition in enzyme-DNA interaction from nonspecific to specific interaction, suggesting that there is a temporal order for formation of specific contacts.


    Related Citations: 
    • Structure of the bacteriophage T4 DNA adenine methyltransferase
      Yang, Z.,Horton, J.R.,Zhou, L.,Zhang, X.J.,Dong, A.,Zhang, X.,Schlagman, S.L.,Kossykh, V.,Cheng, X.
      (2003) Nat.Struct.Mol.Biol. 10: 849


    Organizational Affiliation

    Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA 30322, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA adenine methylase
A, B
259Enterobacteria phage T4Mutation(s): 0 
Gene Names: DAM
EC: 2.1.1.72
Find proteins for P04392 (Enterobacteria phage T4)
Go to UniProtKB:  P04392
Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*AP*CP*CP*AP*TP*GP*AP*TP*CP*TP*GP*AP*C)-3'C13N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*TP*GP*TP*CP*AP*GP*AP*TP*CP*AP*TP*GP*G)-3'D13N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
SAH
Query on SAH

Download SDF File 
Download CCD File 
A, B
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.214 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 38.900α = 90.00
b = 125.800β = 104.70
c = 73.200γ = 90.00
Software Package:
Software NamePurpose
GLRFphasing
XDSdata scaling
XDSdata reduction
SCALEPACKdata scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-05-17
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description