2HMY

BINARY COMPLEX OF HHAI METHYLTRANSFERASE WITH ADOMET FORMED IN THE PRESENCE OF A SHORT NONPSECIFIC DNA OLIGONUCLEOTIDE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Work: 0.198 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

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

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

(1999) J Mol Biol 287: 201-209

  • DOI: 10.1006/jmbi.1999.2608
  • Primary Citation of Related Structures:  
    2HMY

  • PubMed 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) ...

    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.


    Related Citations: 
    • 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
    • Purification, crystallization, and preliminary X-ray diffraction analysis of an M.HhaI-AdoMet complex.
      Kumar, S., Cheng, X., Pflugrath, J.W., Roberts, R.J.
      (1992) Biochemistry 31: 8648

    Organizational Affiliation

    Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA, 30322, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (CYTOSINE-SPECIFIC METHYLTRANSFERASE HHAI)A [auth B]327Haemophilus haemolyticusMutation(s): 0 
EC: 2.1.1.73 (PDB Primary Data), 2.1.1.37 (UniProt)
UniProt
Find proteins for P05102 (Haemophilus parahaemolyticus)
Explore P05102 
Go to UniProtKB:  P05102
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAM (Subject of Investigation/LOI)
Query on SAM

Download Ideal Coordinates CCD File 
BS-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Work: 0.198 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.3α = 90
b = 74.68β = 103
c = 90.96γ = 90
Software Package:
Software NamePurpose
PHASESphasing
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-03-19
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-11-06
    Changes: Data collection, Database references