1HMY | pdb_00001hmy

CRYSTAL STRUCTURE OF THE HHAI DNA METHYLTRANSFERASE COMPLEXED WITH S-ADENOSYL-L-METHIONINE

• PDB DOI: https://doi.org/10.2210/pdb1HMY/pdb

• Classification: TRANSFERASE(METHYLTRANSFERASE)
• Organism(s): Haemophilus haemolyticus
• Mutation(s): No 


• Deposited: 1993-08-05 Released: 1993-10-31 
• Deposition Author(s): Cheng, X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Work: 
  0.200 (Depositor) 
• R-Value Observed: 
  0.200 (Depositor) 

Literature

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: 299-307

• PubMed: 8343957 
• DOI: https://doi.org/10.1016/0092-8674(93)90421-l
• Primary Citation Related Structures: 
  1HMY


• PubMed Abstract: 
  

  The first three-dimensional structure of a DNA methyltransferase is presented. The crystal structure of the DNA (cytosine-5)-methyltransferase, M.HhaI (recognition sequence: GCGC), complexed with S-adenosyl-L-methionine has been determined and refined at 2.5 A resolution. The core of the structure is dominated by sequence motifs conserved among all DNA (cytosine-5)-methyltransferases, and these are responsible for cofactor binding and methyltransferase function.

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Organizational Affiliation: 
• W. M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, New York 11724.

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: 2,633 
• Modeled Residue Count: 327 
• Deposited Residue Count: 327 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HaeIII METHYLTRANSFERASE	A	327	Haemophilus haemolyticus	Mutation(s): 0  EC: 2.1.1.37
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 [auth A]	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Work:  0.200 (Depositor) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.3	α = 90
b = 72.7	β = 102.5
c = 91	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1993-10-31 
Deposition Author(s): Cheng, X.

Revision History  

• Version 1.0: 1993-10-31
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2012-02-01
  Changes: Structure summary
• Version 1.4: 2024-06-05
  Changes: Data collection, Database references, Derived calculations, Other
• Version 1.5: 2024-12-25
  Changes: Advisory, Derived calculations, Structure summary