PDBsum entry: 9mht

Transferase/DNA

PDB id: 9mht

Contents

Protein chain

327 a.a. *

DNA/RNA

Ligands

SAH

Waters ×242

* Residue conservation analysis

PDB id:

9mht

Name:

Transferase/DNA

Title:

Cytosine-specific methyltransferase hhai/DNA complex

Structure:

5'-d(p Cp Cp Ap Tp Gp Cp Gp Cp Tp Gp Ap C)-3'. Chain: c. Engineered: yes. 5'-d(p Gp Tp Cp Ap Gp (3Dr)p Gp Cp Ap Tp Gp G)- 3'. Chain: d. Engineered: yes. Cytosine-specific methyltransferase hhai. Chain: a.

Source:

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

Biol. unit:

Nonamer (from PQS)

Resolution:

2.39Å R-factor: 0.186

Authors:

M.O'Gara,J.R.Horton,R.J.Roberts,X.Cheng

Key ref:

M.O'Gara et al. (1998). Structures of HhaI methyltransferase complexed with substrates containing mismatches at the target base. Nat Struct Biol, 5, 872-877. PubMed id: 9783745 DOI: 10.1038/2312

Date:

07-Aug-98 Release date: 01-Dec-98

Protein chain

P05102  (MTH1_HAEPH) -  Modification methylase HhaI

Seq: 327 a.a.

Struc: 327 a.a.

Enzyme reactions

• Enzyme class: E.C.2.1.1.37 - Dna (cytosine-5-)-methyltransferase.
• Reaction: S-adenosyl-L-methionine + DNA = S-adenosyl-L-homocysteine + DNA containing 5-methylcytosine

S-adenosyl-L-methionine + DNA = S-adenosyl-L-homocysteine (Bound ligand (Het Group name = SAH) corresponds exactly) + DNA containing 5-methylcytosine

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

 Gene Ontology (GO) functional annotation 

• Biological process: DNA restriction-modification system (2 terms)
• Biochemical function: transferase activity (4 terms)

reference

DOI no: 10.1038/2312

Nat Struct Biol 5:872-877 (1998)

PubMed id: 9783745

Structures of HhaI methyltransferase complexed with substrates containing mismatches at the target base.

M.O'Gara, J.R.Horton, R.J.Roberts, X.Cheng.

ABSTRACT

Three structures have been determined for complexes between HhaI methyltransferase (M.HhaI) and oligonucleotides containing a G:A, G:U or G:AP (AP = abasic or apurinic/apyrimidinic) mismatch at the target base pair. The mismatched adenine, uracil and abasic site are all flipped out of the DNA helix and located in the enzyme's active-site pocket, adopting the same conformation as in the flipped-out normal substrate. These results, particularly the flipped-out abasic deoxyribose sugar, provide insight into the mechanism of base flipping. If the process involves the protein pushing the base out of the helix, then the push must take place not on the base, but rather on the sugar-phosphate backbone. Thus rotation of the DNA backbone is probably the key to base flipping.

Selected figure(s)

Figure 1.
Figure 1. a, Close up of the 5'-GCGC-3'/5'-GXGC-3' sequence, where X = A (top), U (middle), and AP (bottom). The difference electron density (F[o] - F[c], [c]), calculated using Phases^37 and displayed using O^38, is shown in green and contoured at 5.0 above the mean, where the mismatched nucleotide (adenine, uracil, or abasic site) was omitted in the structure factor (F[c], [c]) calculation. b, Ribbon^39 diagram of the complex of M.HhaI (in black) bound to a DNA duplex containing an abasic site. The DNA is in magenta, with six phosphates and sugar rings in green: three on the 5' side and three on the 3' side of the abasic site. Arg 165 is also shown in black. c, Phosphodiester backbone contacts between M.HhaI and the oligonucleotide containing an abasic site. The distance cut off is 3.0 Å for hydrogen bonds (solid lines) and 3.35 Å for non-bonded contacts (dashed lines). The phosphate groups and water molecules are labeled as 'P' and 'W' respectively. Mainly, interactions involve six phosphates (white letter P on black background) of the damaged strand: three on the 5' side and three on the 3' side of the flipped site. The figure was modified from the output of NUCPLOT^40. For specific base contacts between M.HhaI and DNA, see Fig. 8 of ref. 1.

Figure 3.
Figure 3. M.HhaI-AdoHcy-G:U mismatch. a, Detailed structure in the vicinity of the mismatched uracil. Color scheme and labeling are the same as in Fig. 2a. The hydrogen atom at the N3 position of uracil was built using X-PLOR^36. The flipped cytosine (in black sticks) of the M.HhaI-AdoHcy-G:C complex^18 is superimposed on the flipped uracil. b, A view perpendicular to (a), looking edge-on to the flipped uracil ring.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (1998, 5, 872-877) copyright 1998.

Figures were selected by the author.