1G38

ADENINE-SPECIFIC METHYLTRANSFERASE M. TAQ I/DNA COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Structure of the N6-adenine DNA methyltransferase M.TaqI in complex with DNA and a cofactor analog.

Goedecke, K.Pignot, M.Goody, R.S.Scheidig, A.J.Weinhold, E.

(2001) Nat.Struct.Mol.Biol. 8: 121-125

  • DOI: 10.1038/84104
  • Also Cited By: 2JG3

  • PubMed Abstract: 
  • The 2.0 A crystal structure of the N6-adenine DNA methyltransferase M.TaqI in complex with specific DNA and a nonreactive cofactor analog reveals a previously unrecognized stabilization of the extrahelical target base. To catalyze the transfer of the ...

    The 2.0 A crystal structure of the N6-adenine DNA methyltransferase M.TaqI in complex with specific DNA and a nonreactive cofactor analog reveals a previously unrecognized stabilization of the extrahelical target base. To catalyze the transfer of the methyl group from the cofactor S-adenosyl-l-methionine to the 6-amino group of adenine within the double-stranded DNA sequence 5'-TCGA-3', the target nucleoside is rotated out of the DNA helix. Stabilization of the extrahelical conformation is achieved by DNA compression perpendicular to the DNA helix axis at the target base pair position and relocation of the partner base thymine in an interstrand pi-stacked position, where it would sterically overlap with an innerhelical target adenine. The extrahelical target adenine is specifically recognized in the active site, and the 6-amino group of adenine donates two hydrogen bonds to Asn 105 and Pro 106, which both belong to the conserved catalytic motif IV of N6-adenine DNA methyltransferases. These hydrogen bonds appear to increase the partial negative charge of the N6 atom of adenine and activate it for direct nucleophilic attack on the methyl group of the cofactor.


    Related Citations: 
    • DIFFERENTIAL BINDING OF S-ADENOSYLMETHIONINE, S-ADENOSYLHOMOCYSTEINE AND SINEFUNGIN TO THE ADENINE-SPECIFIC DNA METHYLTRANSFERASE M. TAQ I
      Schluckebier, G.,Kozak, M.,Bleimling, N.,Weinhold, E.,Saenger, W.
      (1997) J.Mol.Biol. 265: 56


    Organizational Affiliation

    Max-Planck-Institut für molekulare Physiologie, Abteilung Physikalische Biochemie, Otto-Hahn-Str. 11, D-44227 Dortmund, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
MODIFICATION METHYLASE TAQI
A, D
393Thermus aquaticusGene Names: taqIM
EC: 2.1.1.72
Find proteins for P14385 (Thermus aquaticus)
Go to UniProtKB:  P14385
Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*GP*TP*TP*CP*GP*AP*TP*GP*TP*C)-3'B,E10N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*GP*AP*CP*AP*TP*CP*GP*(6MA)P*AP*C)-3'C,F10N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NEA
Query on NEA

Download SDF File 
Download CCD File 
A, D
5'-DEOXY-5'-[2-(AMINO)ETHYLTHIO]ADENOSINE
C12 H18 N6 O3 S
APAPOJUCRZTCHD-WOUKDFQISA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
6MA
Query on 6MA
C, F
DNA LINKINGC11 H16 N5 O6 PA
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.196 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 59.500α = 90.00
b = 68.650β = 92.20
c = 114.430γ = 90.00
Software Package:
Software NamePurpose
MAR345data collection
XDSdata reduction
CNSrefinement
AMoREphasing
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-03-05
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2013-08-28
    Type: Atomic model
  • Version 1.4: 2017-10-04
    Type: Advisory, Refinement description