2ADM

ADENINE-N6-DNA-METHYLTRANSFERASE TAQI


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Differential binding of S-adenosylmethionine S-adenosylhomocysteine and Sinefungin to the adenine-specific DNA methyltransferase M.TaqI.

Schluckebier, G.Kozak, M.Bleimling, N.Weinhold, E.Saenger, W.

(1997) J.Mol.Biol. 265: 56-67

  • DOI: 10.1006/jmbi.1996.0711
  • Primary Citation of Related Structures:  1AQI, 1AQJ
  • Also Cited By: 2IBS, 2IBT

  • PubMed Abstract: 
  • The crystal structures of the binary complexes of the DNA methyltransferase M.TaqI with the inhibitor Sinefungin and the reaction product S-adenosyl-L-homocysteine were determined, both at 2.6 A resolution. Structural comparison of these binary compl ...

    The crystal structures of the binary complexes of the DNA methyltransferase M.TaqI with the inhibitor Sinefungin and the reaction product S-adenosyl-L-homocysteine were determined, both at 2.6 A resolution. Structural comparison of these binary complexes with the complex formed by M.TaqI and the cofactor S-adenosyl-L-methionine suggests that the key element for molecular recognition of these ligands is the binding of their adenosine part in a pocket, and discrimination between cofactor, reaction product and inhibitor is mediated by different conformations of these molecules; the methionine part of S-adenosyl-L-methionine is located in the binding cleft, whereas the amino acid moieties of Sinefungin and S-adenosyl-L-homocysteine are in a different orientation and interact with the active site amino acid residues 105NPPY108. Dissociation constants for the complexes of M.TaqI with the three ligands were determined spectrofluorometrically. Sinefungin binds more strongly than S-adenosyl-L-homocysteine or S-adenosyl-L-methionine, with KD=0.34 microM, 2.4 microM and 2.0 microM, respectively.


    Related Citations: 
    • Universal Catalytic Domain Structure of Adomet-Dependent Methyltransferases
      Schluckebier, G.,O'Gara, M.,Saenger, W.,Cheng, X.
      (1995) J.Mol.Biol. 247: 16
    • Three-Dimensional Structure of the Adenine-Specific DNA Methyltransferase M.Taq I in Complex with the Cofactor S-Adenosylmethionine
      Labahn, J.,Granzin, J.,Schluckebier, G.,Robinson, D.P.,Jack, W.E.,Schildkraut, I.,Saenger, W.
      (1994) Proc.Natl.Acad.Sci.USA 91: 10957
    • A Model for DNA Binding and Enzyme Action Derived from Crystallographic Studies of the TaqI N6-Adenine-Methyltransferase
      Schluckebier, G.,Labahn, J.,Granzin, J.,Schildkraut, I.,Saenger, W.
      (1995) Gene 157: 131


    Organizational Affiliation

    Institut für Kristallographie Freie Universität Berlin, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ADENINE-N6-DNA-METHYLTRANSFERASE TAQI
A, B
421Thermus aquaticusGene Names: taqIM
EC: 2.1.1.72
Find proteins for P14385 (Thermus aquaticus)
Go to UniProtKB:  P14385
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAM
Query on SAM

Download SDF File 
Download CCD File 
A, B
S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
SAMKd: 2000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.214 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 130.660α = 90.00
b = 141.830β = 90.00
c = 53.150γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
X-PLORmodel building
DENZOdata reduction
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-01-27
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance