1G38

ADENINE-SPECIFIC METHYLTRANSFERASE M. TAQ I/DNA COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.208 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.5 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 Biol 8: 121-125

  • DOI: https://doi.org/10.1038/84104
  • Primary Citation of Related Structures:  
    1G38

  • 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 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.


  • Organizational Affiliation

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


Macromolecules

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
MODIFICATION METHYLASE TAQIE [auth A],
F [auth D]
393Thermus aquaticusMutation(s): 0 
EC: 2.1.1.72
UniProt
Find proteins for P14385 (Thermus aquaticus)
Explore P14385 
Go to UniProtKB:  P14385
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14385
Sequence Annotations
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  • Reference Sequence

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Entity ID: 1
MoleculeChains LengthOrganismImage
5'-D(*GP*TP*TP*CP*GP*AP*TP*GP*TP*C)-3'A [auth B],
C [auth E]
10N/A
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
5'-D(*GP*AP*CP*AP*TP*CP*GP*(6MA)P*AP*C)-3'B [auth C],
D [auth F]
10N/A
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NEA
Query on NEA

Download Ideal Coordinates CCD File 
G [auth A],
H [auth D]
5'-DEOXY-5'-[2-(AMINO)ETHYLTHIO]ADENOSINE
C12 H18 N6 O3 S
APAPOJUCRZTCHD-WOUKDFQISA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.208 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.5α = 90
b = 68.65β = 92.2
c = 114.43γ = 90
Software Package:
Software NamePurpose
MAR345data collection
XDSdata reduction
AMoREphasing
CNSrefinement
XDSdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-03-05
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2013-08-28
    Changes: Atomic model
  • Version 1.4: 2017-10-04
    Changes: Advisory, Refinement description
  • Version 1.5: 2023-08-09
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description