Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 45.16 kDa 
• Atom Count: 3144 
• Modelled Residue Count: 352 
• Deposited Residue Count: 352 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

1MHT

COVALENT TERNARY STRUCTURE OF HHAI METHYLTRANSFERASE, DNA AND S-ADENOSYL-L-HOMOCYSTEINE

• DOI: 10.2210/pdb1MHT/pdb
• NDB: PDEB08

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


• Deposited: 1994-12-08 Released: 1995-06-03 
• Deposition Author(s): Cheng, X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Work: 0.174 
• R-Value Observed: 0.174 

Literature

HhaI methyltransferase flips its target base out of the DNA helix.

Klimasauskas, S., Kumar, S., Roberts, R.J., Cheng, X.

(1994) Cell 76: 357-369

• PubMed: 8293469 
• DOI: 10.1016/0092-8674(94)90342-5
• Primary Citation of Related Structures:  
  1MHT


• PubMed Abstract: 
  

The crystal structure has been determined at 2.8 A resolution for a chemically-trapped covalent reaction intermediate between the HhaI DNA cytosine-5-methyltransferase, S-adenosyl-L-homocysteine, and a duplex 13-mer DNA oligonucleotide containing methylated 5-fluorocytosine at its target. The DNA is located in a cleft between the two domains of the protein and has the characteristic conformation of B-form DNA, except for a disrupted G-C base pair that contains the target cytosine. The cytosine residue has swung completely out of the DNA helix and is positioned in the active site, which itself has undergone a large conformational change. The DNA is contacted from both the major and the minor grooves, but almost all base-specific interactions between the enzyme and the recognition bases occur in the major groove, through two glycine-rich loops from the small domain. The structure suggests how the active nucleophile reaches its target, directly supports the proposed mechanism for cytosine-5 DNA methylation, and illustrates a novel mode of sequence-specific DNA recognition.

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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

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Organizational Affiliation: 

W. M. Keck Structural Biology Laboratory, Cold Spring Harbor, New York 11724.

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (HHAI METHYLTRANSFERASE)	C [auth A]	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

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*GP*AP*TP*AP*GP*(C36)P*GP*CP*TP*AP*TP*C)-3')	A [auth B]	12	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*GP*AP*TP*AP*GP*(C36)P*GP*CP*TP*AP*TP*C)-3')	B [auth C]	13	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH (Subject of Investigation/LOI)	D [auth A]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Work: 0.174 
• R-Value Observed: 0.174 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.86	α = 90
b = 99.86	β = 90
c = 325.2	γ = 120

Software Package:

Software Name	Purpose
X-PLOR	refinement
MADNES	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1994-12-08 
• Released Date: 1995-06-03 
Deposition Author(s): Cheng, X.

Revision History  

• Version 1.0: 1995-06-03
  Type: Initial release
  
• Version 1.1: 2008-05-22
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-04-18
  Changes: Data collection