2IBS

Crystal structure of the adenine-specific DNA methyltransferase M.TaqI complexed with the cofactor analog AETA and a 10 bp DNA containing 2-aminopurine at the target position

PDB DOI: 10.2210/pdb2IBS/pdb
NDB: PD0867

Classification: TRANSFERASE/DNA
Organism(s): Thermus aquaticus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2006-09-12 Released: 2007-05-29
Deposition Author(s): Pljevaljcic, G., Lenz, T., Scheidig, A.J., Weinhold, E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.252
R-Value Work: 0.195
R-Value Observed: 0.198

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

2-Aminopurine Flipped into the Active Site of the Adenine-Specific DNA Methyltransferase M.TaqI: Crystal Structures and Time-Resolved Fluorescence

Lenz, T., Bonnist, E.Y.M., Pljevaljcic, G., Neely, R.K., Dryden, D.T.F., Scheidig, A.J., Jones, A.C., Weinhold, E.

(2007) J Am Chem Soc 129: 6240-6248

PubMed: 17455934 Search on PubMed
DOI: 10.1021/ja069366n
Primary Citation of Related Structures:
2IBS, 2IBT

PubMed Abstract:

We report the crystal structure of the DNA adenine-N6 methyltransferase, M.TaqI, complexed with DNA, showing the fluorescent adenine analog, 2-aminopurine, flipped out of the DNA helix and occupying virtually the same position in the active site as the natural target adenine. Time-resolved fluorescence spectroscopy of the crystalline complex faithfully reports this state: base flipping is accompanied by the loss of the very short ( approximately 50 ps) lifetime component associated with fully base-stacked 2-aminopurine in DNA, and 2-aminopurine is subject to considerable quenching by pi-stacking interactions with Tyr108 in the catalytic motif IV (NPPY). This proves 2-aminopurine to be an excellent probe for studying base flipping by M.TaqI and suggests similar quenching in the active sites of DNA and RNA adenine-N6 as well as DNA cytosine-N4 methyltransferases sharing the conserved motif IV. In solution, the same distinctive fluorescence response confirms complete destacking from DNA and is also observed when the proposed key residue for base flipping by M.TaqI, the target base partner thymine, is substituted by an abasic site analog. The corresponding cocrystal structure shows 2-aminopurine in the active site of M.TaqI, demonstrating that the partner thymine is not essential for base flipping. However, in this structure, a shift of the 3' neighbor of the target base into the vacancy left after base flipping is observed, apparently replicating a stabilizing role of the missing partner thymine. Time-resolved fluorescence and acrylamide quenching measurements of M.TaqI complexes in solution provide evidence for an alternative binding site for the extra-helical target base within M.TaqI and suggest that the partner thymine assists in delivering the target base into the active site.

Related Citations:

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

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

Organizational Affiliation:

Institute of Organic Chemistry, RWTH Aachen University, Landoltweg 1, D-52056 Aachen, Germany.

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Modification methylase TaqI	E [auth A], F [auth D]	421	Thermus aquaticus	Mutation(s): 0 Gene Names: taqIM EC: 2.1.1.72
UniProt
Find proteins for P14385 (Thermus aquaticus) Explore P14385 Go to UniProtKB: P14385
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P14385
Protein Feature View Expand
Reference Sequence

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Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(GPTPTPCPGP(2PR)PTPGPTPC)-3'	A [auth B], C [auth E]	10	N/A
Protein Feature View Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(GPAPCPAPTPCPGP(6MA)PAPC)-3'	B [auth C], D [auth F]	10	N/A
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NEA Query on NEA Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth D] MOL2 format, chain G [auth A] MOL2 format, chain H [auth D]	G [auth A], H [auth D]	5'-DEOXY-5'-[2-(AMINO)ETHYLTHIO]ADENOSINE C₁₂ H₁₈ N₆ O₃ S APAPOJUCRZTCHD-WOUKDFQISA-N		Ligand Interaction