Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 45155.68 
• Atom Count: 3144 
• 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 parahaemolyticus


• 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: 2.6 Å
• R-Value Work: 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 


• 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

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
PROTEIN (HHAI METHYLTRANSFERASE)	A	327	Haemophilus parahaemolyticus	Mutation(s): 0  Gene Names: hhaIM EC: 2.1.1.37
Find proteins for P05102 (Haemophilus parahaemolyticus) Go to UniProtKB:  P05102

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

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
SAH	A	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
C36	B, C	DNA LINKING	C10 H17 F N3 O8 P		DC

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.6 Å
• R-Value Work: 0.174 
• Space Group: H 3 2

Unit Cell:

Length (Å)	Angle (°)
a = 99.860	α = 90.00
b = 99.860	β = 90.00
c = 325.200	γ = 120.00

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
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance
• Version 1.3: 2018-04-18
  Type: Data collection