2HMY | pdb_00002hmy

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

• PDB DOI: https://doi.org/10.2210/pdb2HMY/pdb

• Classification: TRANSFERASE (METHYLTRANSFERASE)
• Organism(s): Haemophilus haemolyticus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1999-02-08 Released: 1999-03-19 
• Deposition Author(s): O'Gara, M., Zhang, X., Roberts, R.J., Cheng, X.

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Experimental Data Snapshot

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

Starting Model: experimental

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 Biology 287: 201-209

• PubMed: 10080885 
• DOI: https://doi.org/10.1006/jmbi.1999.2608
• Primary Citation 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). 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.

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 37.44 kDa 
• Atom Count: 2,696 
• Modeled Residue Count: 327 
• Deposited Residue Count: 327 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (CYTOSINE-SPECIFIC METHYLTRANSFERASE HHAI)	A [auth B]	327	Haemophilus haemolyticus	Mutation(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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAM	B	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N

Experimental Data & Validation

Experimental Data

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

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.3	α = 90
b = 74.68	β = 103
c = 90.96	γ = 90

Software Package:

Software Name	Purpose
PHASES	phasing
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-03-19 
Deposition Author(s): O'Gara, M., Zhang, X., Roberts, R.J., Cheng, X.

Revision History  

• 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
• Version 1.4: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description