Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 102818.48 
• Atom Count: 7232 
• Residue Count: 826 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

1G38

ADENINE-SPECIFIC METHYLTRANSFERASE M. TAQ I/DNA COMPLEX

• DOI: 10.2210/pdb1G38/pdb
• NDB: PD0188

• Classification: TRANSFERASE/DNA
• Organism(s): Thermus aquaticus
• Expression System: Escherichia coli


• Deposited: 2000-10-23 Released: 2001-03-05 
• Deposition Author(s): Goedecke, K., Pignot, M., Goody, R.S., Scheidig, A.J., Weinhold, E.

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Experimental Data Snapshot

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

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

• PubMed: 11175899 
• 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 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.

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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




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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
Molecule	Chains	Sequence Length	Organism	Details
MODIFICATION METHYLASE TAQI	A, D	393	Thermus aquaticus	Mutation(s): 0  Gene Names: taqIM EC: 2.1.1.72
Find proteins for P14385 (Thermus aquaticus) Go to UniProtKB:  P14385

Entity ID: 1
Molecule	Chains	Length	Organism
5'-D(*GP*TP*TP*CP*GP*AP*TP*GP*TP*C)-3'	B,E	10	N/A

Entity ID: 2
Molecule	Chains	Length	Organism
5'-D(*GP*AP*CP*AP*TP*CP*GP*(6MA)P*AP*C)-3'	C,F	10	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
NEA	A, D	5'-DEOXY-5'-[2-(AMINO)ETHYLTHIO]ADENOSINE C12 H18 N6 O3 S APAPOJUCRZTCHD-WOUKDFQISA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
6MA	C, F	DNA LINKING	C11 H16 N5 O6 P		A

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 = 59.500	α = 90.00
b = 68.650	β = 92.20
c = 114.430	γ = 90.00

Software Package:

Software Name	Purpose
MAR345	data collection
XDS	data reduction
CNS	refinement
AMoRE	phasing
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2000-10-23 
• Released Date: 2001-03-05 
• Deposition Author(s): Goedecke, K., Pignot, M., Goody, R.S., Scheidig, A.J., Weinhold, E.

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