PDBsum entry 2c7q

Transferase/DNA

PDB id: 2c7q

Contents

Protein chain

327 a.a. *

DNA/RNA

Ligands

SAH

SO4 ×3

CIT

Waters ×366

* Residue conservation analysis

PDB id:

2c7q

Name:

Transferase/DNA

Title:

Hhai DNA methyltransferase complex with oligonucleotide containing 2- aminopurine outside the recognition sequence (paired with g) and sah

Structure:

Modification methylase hhai. Chain: a. Synonym: DNA methyltransferase hhai, cytosine-specific methyltransferase hhai. Engineered: yes. 5'-d( T Gp Gp (2Pr) Gp Gp (5Cm) Gp Cp Tp Gp Ap C)-3'. Chain: c. Engineered: yes. 5'-d( T Gp Tp Cp Ap Gp Cp Gp Cp Cp Gp Cp C)-3'.

Source:

Haemophilus haemolyticus. Organism_taxid: 726. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Synthetic construct. Organism_taxid: 32630. Organism_taxid: 32630

Biol. unit:

Trimer (from PDB file)

Resolution:

1.85Å R-factor: 0.187 R-free: 0.210

Authors:

D.Daujotyte,S.Grazulis

Key ref:

R.K.Neely et al. (2005). Time-resolved fluorescence of 2-aminopurine as a probe of base flipping in M.HhaI-DNA complexes. Nucleic Acids Res, 33, 6953-6960. PubMed id: 16340006

Date:

27-Nov-05 Release date: 14-Dec-05

Protein chain

P05102  (MTH1_HAEPH) -  Type II methyltransferase M.HhaI from Haemophilus parahaemolyticus

Seq: 327 a.a.

Struc: 327 a.a.

DNA/RNA chains

T-G-G-2PR-G-G-5CM-G-C-T-G-A-C 13 bases

G-T-C-A-G-C-G-C-C-G-C-C 12 bases

Enzyme reactions

• Enzyme class: E.C.2.1.1.37 - Dna (cytosine-5-)-methyltransferase.
• Reaction: a 2'-deoxycytidine in DNA + S-adenosyl-L-methionine = a 5-methyl- 2'-deoxycytidine in DNA + S-adenosyl-L-homocysteine + H⁺

2'-deoxycytidine in DNA + S-adenosyl-L-methionine = 5-methyl- 2'-deoxycytidine in DNA + S-adenosyl-L-homocysteine + H(+) (Bound ligand (Het Group name = SAH) corresponds exactly)

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

Added reference

Nucleic Acids Res 33:6953-6960 (2005)

PubMed id: 16340006

Time-resolved fluorescence of 2-aminopurine as a probe of base flipping in M.HhaI-DNA complexes.

R.K.Neely, D.Daujotyte, S.Grazulis, S.W.Magennis, D.T.Dryden, S.Klimasauskas, A.C.Jones.

ABSTRACT

DNA base flipping is an important mechanism in molecular enzymology, but its study is limited by the lack of an accessible and reliable diagnostic technique. A series of crystalline complexes of a DNA methyltransferase, M.HhaI, and its cognate DNA, in which a fluorescent nucleobase analogue, 2-aminopurine (AP), occupies defined positions with respect the target flipped base, have been prepared and their structures determined at higher than 2 A resolution. From time-resolved fluorescence measurements of these single crystals, we have established that the fluorescence decay function of AP shows a pronounced, characteristic response to base flipping: the loss of the very short (approximately 100 ps) decay component and the large increase in the amplitude of the long (approximately 10 ns) component. When AP is positioned at sites other than the target site, this response is not seen. Most significantly, we have shown that the same clear response is apparent when M.HhaI complexes with DNA in solution, giving an unambiguous signal of base flipping. Analysis of the AP fluorescence decay function reveals conformational heterogeneity in the DNA-enzyme complexes that cannot be discerned from the present X-ray structures.

Selected figure(s)

Figure 2.
Detailed view of the H-bond interactions between the M.HhaI enzyme and the APtarget duplex. DNA and protein residues are shown as sticks, a bound solvent molecule (presumed water) is shown as a red ball.

Figure 3.
Interaction of M.HhaI with duplexes where AP is opposite or adjacent to the target base. (a) The sequences of the 10 bp at the centre of the APadj duplex (left) and APopp duplex (right). Bases in the M.HhaI recognition sequence are shown in boldface/italic; the target base is circled; AP is denoted P and is in red; M is 5-methyl cytosine (used to direct enzyme binding to the opposite strand of the duplex). (b) Crystal structures of the complexes of the M.HhaI enzyme with the APadj duplex (left) and the APopp duplex (right), showing the molecular structure in the vicinity of the recognition sequence. (c) Detailed view of the H-bond interactions between the M.HhaI enzyme and the APadj duplex (left) and the APopp duplex (right).

Figures were selected by an automated process.