3MHT

TERNARY STRUCTURE OF HHAI METHYLTRANSFERASE WITH UNMODIFIED DNA AND ADOHCY


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Enzymatic C5-cytosine methylation of DNA: mechanistic implications of new crystal structures for HhaL methyltransferase-DNA-AdoHcy complexes.

O'Gara, M.Klimasauskas, S.Roberts, R.J.Cheng, X.

(1996) J.Mol.Biol. 261: 634-645

  • Primary Citation of Related Structures:  4MHT

  • PubMed Abstract: 
  • The refined crystal structures of HhaI methyltransferase complexed with cognate unmethylated or methylated DNA together with S-adenosyl-L-homocysteine, along with the previously-solved binary and covalent ternary structures, offer a detailed picture ...

    The refined crystal structures of HhaI methyltransferase complexed with cognate unmethylated or methylated DNA together with S-adenosyl-L-homocysteine, along with the previously-solved binary and covalent ternary structures, offer a detailed picture of the active site at individual stages throughout the reaction cycle. This picture supports and extends a proposed mechanism for C5-cytosine methylation that may be general for the whole family of C5-cytosine methyltransferases. The structures of the two new complexes have been refined to crystallographic R-factors of 0.189 and 0.178, respectively, at 2.7 A resolution. We observe that both unmethylated 2'-deoxycytidine and 5-methyl-2'-deoxycytidine flip out of the DNA helix and fit into the active site of the enzyme. The catalytic sulfur atom of Cys81 interacts strongly with C6. The C5 methyl group of the flipped 5-methyl-2'-deoxycytidine is bent approximately 50 degrees out of the plane of the cytosine ring and towards the sulfur atom of S-adenosyl-L-homocysteine. This unusual position is probably due to partial sp3 character at C5 and C6 and to steric effects of the conserved amino acid residues Pro80 and Cys81. Two water molecules are held near the hydrophobic edge (C5 and C6) of the flipped cytosine by two conserved amino acid residues (Gln82 and Asn304) and the phosphoryl oxygen atom of the phosphate group 3' to the flipped nucleotide, and one of them may serve as the general base for eliminating the proton from C5. Protonation of the cytosine N3 during the methylation reaction may involve Glu119, which itself might be protonated via a water-mediated interaction between the terminal carboxyl group of Glu119 and the amino group of the methionine moiety of S-adenosyl-L-methionine. The cofactor thus plays two key roles in the reaction.


    Related Citations: 
    • HhaI Methyltransferase Flips its Target Base Out of the DNA Helix
      Klimasauskas, S.,Kumar, S.,Roberts, R.J.,Cheng, X.
      (1994) Cell 76: 357
    • Crystal Structure of the HhaI DNA Methyltransferase Complexed with S-Adenosyl- L-Methionine
      Cheng, X.,Kumar, S.,Posfai, J.,Pflugrath, J.W.,Roberts, R.J.
      (1993) Cell 74: 299


    Organizational Affiliation

    W.M. Keck Structural Biology Laboratory Cold Spring Harbor Laboratory, NY 11724, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (HHAI METHYLTRANSFERASE (E.C.2.1.1.73))
A
327Haemophilus parahaemolyticusGene Names: hhaIM
EC: 2.1.1.37
Find proteins for P05102 (Haemophilus parahaemolyticus)
Go to UniProtKB:  P05102
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*AP*TP*AP*GP*CP*GP*CP*TP*AP*TP*C)-3')C12N/A
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*GP*AP*TP*AP*GP*CP*GP*CP*TP*AP*TP*C)-3')D13N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAH
Query on SAH

Download SDF File 
Download CCD File 
A
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Work: 0.189 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 99.860α = 90.00
b = 99.860β = 90.00
c = 325.200γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-01-27
    Type: Initial release
  • Version 1.1: 2008-05-22
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance