1Q0T

Ternary Structure of T4DAM with AdoHcy and DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.238 

wwPDB Validation   3D Report Full Report


This is version 1.3 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 Biol 10: 849-855

  • DOI: 10.1038/nsb973
  • Primary Citation of Related Structures:  
    1Q0T, 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 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 ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA adenine methylaseC [auth A], D [auth B]259Escherichia virus T4Mutation(s): 0 
Gene Names: DAM
EC: 2.1.1.72
Find proteins for P04392 (Enterobacteria phage T4)
Explore P04392 
Go to UniProtKB:  P04392
Protein Feature View
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-D(*AP*CP*AP*GP*GP*AP*TP*CP*CP*TP*GP*T)-3'A [auth C], B [auth D]12N/A
    Small Molecules
    Ligands 2 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    SAH
    Query on SAH

    Download Ideal Coordinates CCD File 
    G [auth A], H [auth B]S-ADENOSYL-L-HOMOCYSTEINE
    C14 H20 N6 O5 S
    ZJUKTBDSGOFHSH-WFMPWKQPSA-N
     Ligand Interaction
    IOD
    Query on IOD

    Download Ideal Coordinates CCD File 
    E [auth C], F [auth D]IODIDE ION
    I
    XMBWDFGMSWQBCA-UHFFFAOYSA-M
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 3.10 Å
    • R-Value Free: 0.293 
    • R-Value Work: 0.238 
    • Space Group: P 1 21 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 39.7α = 90
    b = 109.7β = 104.2
    c = 73.6γ = 90
    Software Package:
    Software NamePurpose
    HKL-2000data collection
    SCALEPACKdata scaling
    SOLVEphasing
    CNSrefinement
    HKL-2000data reduction

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 2003-09-23
      Type: Initial release
    • Version 1.1: 2008-04-29
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance
    • Version 1.3: 2020-07-22
      Changes: Derived calculations