1Q0T

Ternary Structure of T4DAM with AdoHcy and DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.238 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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.Hattman, S.Cheng, X.

(2003) Nat.Struct.Mol.Biol. 10: 849-855

  • DOI: 10.1038/nsb973
  • Primary Citation of Related Structures:  1Q0S

  • PubMed Abstract: 
  • DNA-adenine methylation at certain GATC sites plays a pivotal role in bacterial and phage gene expression as well as bacterial virulence. We report here the crystal structures of the bacteriophage T4Dam DNA adenine methyltransferase (MTase) in a bina ...

    DNA-adenine methylation at certain GATC sites plays a pivotal role in bacterial and phage gene expression as well as bacterial virulence. We report here the crystal structures of the bacteriophage T4Dam DNA adenine methyltransferase (MTase) in a binary complex with the methyl-donor product S-adenosyl-L-homocysteine (AdoHcy) and in a ternary complex with a synthetic 12-bp DNA duplex and AdoHcy. T4Dam contains two domains: a seven-stranded catalytic domain that harbors the binding site for AdoHcy and a DNA binding domain consisting of a five-helix bundle and a beta-hairpin that is conserved in the family of GATC-related MTase orthologs. Unexpectedly, the sequence-specific T4Dam bound to DNA in a nonspecific mode that contained two Dam monomers per synthetic duplex, even though the DNA contains a single GATC site. The ternary structure provides a rare snapshot of an enzyme poised for linear diffusion along the DNA.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA adenine methylase
A, B
259Enterobacteria phage T4Gene 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*AP*GP*GP*AP*TP*CP*CP*TP*GP*T)-3'C,D12N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IOD
Query on IOD

Download SDF File 
Download CCD File 
C, D
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 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: 3.1 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.238 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 39.700α = 90.00
b = 109.700β = 104.20
c = 73.600γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
SOLVEphasing
CNSrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-09-23
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance