PDBsum entry: 2hmy

Transferase (methyltransferase)

PDB id: 2hmy

Contents

Protein chain

327 a.a. *

Ligands

SAM

Waters ×63

* Residue conservation analysis

PDB id:

2hmy

Name:

Transferase (methyltransferase)

Title:

Binary complex of hhai methyltransferase with adomet formed in the presence of a short nonpsecific DNA oligonucleotide

Structure:

Protein (cytosine-specific methyltransferase hhai). Chain: b. Engineered: yes

Source:

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

Resolution:

2.61Å R-factor: 0.198

Authors:

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

Key ref:

M.O'Gara et al. (1999). Structure of a binary complex of HhaI methyltransferase with S-adenosyl-L-methionine formed in the presence of a short non-specific DNA oligonucleotide. J Mol Biol, 287, 201-209. PubMed id: 10080885 DOI: 10.1006/jmbi.1999.2608

Date:

08-Feb-99 Release date: 19-Mar-99

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 (Bound ligand (Het Group name = SAM) corresponds exactly) + DNA = S-adenosyl-L-homocysteine + 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: 10.1006/jmbi.1999.2608

J Mol Biol 287:201-209 (1999)

PubMed id: 10080885

Structure of a binary complex of HhaI methyltransferase with S-adenosyl-L-methionine formed in the presence of a short non-specific DNA oligonucleotide.

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

ABSTRACT

We have determined a structure for a complex formed between HhaI methyltransferase (M.HhaI) and S-adenosyl-L-methionine (AdoMet) in the presence of a non-specific short oligonucleotide. M.HhaI binds to the non-specific short oligonucleotides in solution. Although no DNA is incorporated in the crystal, AdoMet binds in a primed orientation, identical with that observed in the ternary complex of the enzyme, cognate DNA, and AdoMet or S-adenosyl-L-homocysteine (AdoHcy). This orientation differs from the previously observed unprimed orientation in the M.HhaI-AdoMet binary complex, where the S+-CH3 unit of AdoMet is protected by a favorable cation-pi interaction with Trp41. The structure suggests that the presence of DNA can guide AdoMet into the primed orientation. These results shed new light on the proposed ordered mechanism of binding and explains the stable association between AdoMet and M.HhaI.

Selected figure(s)

Figure 3.

Figure 4.
Figure 4. Close up of the AdoMet primed orientation in 2HMY. The difference electron densities, (2F[o] − F[c], α[c]) in light blue and (F[o] − F[c], α[c]) in red are contoured at 1.0σ and 3.0σ, respectively, above the mean, where the methyl group was omitted in the structure factor (F[c], α[c]) calculation. F[o] and F[c] are the observed and calculated structure factor amplitudes, respectively. AdoMet is in thick stick representation, with black for carbon, blue for nitrogen, red for oxygen, and green for sulfur. The neighboring M.HhaI amino acid residues are in black thin line representation and labeled with black lettering. The AdoMet methionine moiety is projected backward from the viewer. The figure was prepared with program O [Jones et al 1991].

The above figures are reprinted by permission from Elsevier: J Mol Biol (1999, 287, 201-209) copyright 1999.

Figures were selected by the author.