9MHT

CYTOSINE-SPECIFIC METHYLTRANSFERASE HHAI/DNA COMPLEX

• PDB DOI: https://doi.org/10.2210/pdb9MHT/pdb
• NAKB: 9MHT

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


• Deposited: 1998-08-07 Released: 1998-12-01 
• Deposition Author(s): O'Gara, M., Horton, J.R., Roberts, R.J., Cheng, X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Work: 0.186 
• R-Value Observed: 0.186 

Starting Model: experimental

Literature

Structures of HhaI methyltransferase complexed with substrates containing mismatches at the target base.

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

(1998) Nat Struct Biol 5: 872-877

• PubMed: 9783745 
• DOI: https://doi.org/10.1038/2312
• Primary Citation of Related Structures:  
  7MHT, 8MHT, 9MHT


• PubMed Abstract: 
  

  Three structures have been determined for complexes between HhaI methyltransferase (M.HhaI) and oligonucleotides containing a G:A, G:U or G:AP (AP = abasic or apurinic/apyrimidinic) mismatch at the target base pair. The mismatched adenine, uracil and abasic site are all flipped out of the DNA helix and located in the enzyme's active-site pocket, adopting the same conformation as in the flipped-out normal substrate. These results, particularly the flipped-out abasic deoxyribose sugar, provide insight into the mechanism of base flipping. If the process involves the protein pushing the base out of the helix, then the push must take place not on the base, but rather on the sugar-phosphate backbone. Thus rotation of the DNA backbone is probably the key to base flipping.

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Organizational Affiliation: 

Pfizer Central Research, Discovery Biology, Sandwich, Kent, England.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 44.64 kDa 
• Atom Count: 3,358 
• Modelled Residue Count: 351 
• Deposited Residue Count: 351 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
CYTOSINE-SPECIFIC METHYLTRANSFERASE HHAI	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
5'-D(P*CP*CP*AP*TP*GP*CP*GP*CP*TP*GP*AP*C)-3'	A [auth C]	12	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(P*GP*TP*CP*AP*GP*(3DR)P*GP*CP*AP*TP*GP*G)-3'	B [auth D]	12	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH	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: 2.39 Å
• R-Value Work: 0.186 
• R-Value Observed: 0.186 
• 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
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-12-01 
Deposition Author(s): O'Gara, M., Horton, J.R., Roberts, R.J., Cheng, X.

Revision History  

• Version 1.0: 1998-12-01
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description