PDBsum entry: 1g38

Transferase/DNA

PDB id: 1g38

Contents

Protein chains

393 a.a. *

DNA/RNA

Ligands

NEA ×2

Waters ×496

* Residue conservation analysis

PDB id:

1g38

Name:

Transferase/DNA

Title:

Adenine-specific methyltransferase m. Taq i/DNA complex

Structure:

5'-d( Gp Tp Tp Cp Gp Ap Tp Gp Tp C)-3'. Chain: b, e. Engineered: yes. 5'-d( Gp Ap Cp Ap Tp Cp Gp (6Ma)p Ap C)-3'. Chain: c, f. Engineered: yes. Modification methylase taqi. Chain: a, d. Fragment: residues 21 - 413.

Source:

Synthetic: yes. Thermus aquaticus. Organism_taxid: 271. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Trimer (from PQS)

Resolution:

2.00Å R-factor: 0.196 R-free: 0.234

Authors:

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

Key ref:

K.Goedecke et al. (2001). Structure of the N6-adenine DNA methyltransferase M.TaqI in complex with DNA and a cofactor analog. Nat Struct Biol, 8, 121-125. PubMed id: 11175899 DOI: 10.1038/84104

Date:

23-Oct-00 Release date: 05-Mar-01

Protein chains

P14385  (MTTA_THEAQ) -  Modification methylase TaqI

Seq: 421 a.a.

Struc: 393 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.2.1.1.72 - Site-specific DNA-methyltransferase (adenine-specific).
• Reaction: S-adenosyl-L-methionine + DNA adenine = S-adenosyl-L-homocysteine + DNA 6-methylaminopurine

S-adenosyl-L-methionine + DNA adenine = S-adenosyl-L-homocysteine (Bound ligand (Het Group name = NEA) matches with 77.00% similarity) + DNA 6-methylaminopurine

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 Gene Ontology (GO) functional annotation 

• Biological process: methylation (2 terms)
• Biochemical function: nucleic acid binding (4 terms)

reference

DOI no: 10.1038/84104

Nat Struct Biol 8:121-125 (2001)

PubMed id: 11175899

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

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

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.

Selected figure(s)

Figure 2.
Figure 2. Schematic representation of hydrogen bonds and salt bridges between M TaqI and the DNA substrate. Direct specific contacts between amino acid residues (green background) of the catalytic domain (upper row) and the bases of the double-stranded recognition sequence (red background) are formed within the widened minor groove. Specific contacts involving amino acid residues (green background) of the smaller domain (lower row) are made via the major groove. Note that Lys 116 and Tyr 117 belong to loop I, which was not visible in the crystal structure of M TaqI without DNA^12. Amino acid residues forming nonspecific contacts mainly with phosphodiester groups are shown with a white background. Amino acid residues Gly 295 and Arg 353 (blue background) are involved in DNA compression by interacting with the 5' and 3' phosphodiester groups of the partner thymine (T15). M, N6-methyladenine.

Figure 4.
Figure 4. Structural comparison between the presented ternary complex and the binary complex of M TaqI15 within the active site. a, Face-on view of the extrahelical adenine as in Fig. 3. The extrahelical target adenine, the nonreactive cofactor analog AETA and protein residues from the ternary complex of M TaqI are red, light yellow and light blue, respectively. The natural cofactor AdoMet and protein residues from the binary complex of M TaqI15 are yellow and blue, respectively. b, Edge-on view of the extrahelical adenine from Phe 196 (not shown). Only the extrahelical target adenine (red) and active site residues including Val 21 and Lys 199 (light blue) of M TaqI from the ternary complex and the natural cofactor AdoMet (yellow) from the binary complex are shown.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2001, 8, 121-125) copyright 2001.

Figures were selected by the author.