7MHT

CYTOSINE-SPECIFIC METHYLTRANSFERASE HHAI/DNA COMPLEX

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.87 Å
  • R-Value Work: 0.156 
  • R-Value Observed: 0.156 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


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

  • 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.

    • Organizational Affiliation: 

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


Macromolecules

Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
CYTOSINE-SPECIFIC METHYLTRANSFERASE HHAIC [auth A]327Haemophilus haemolyticusMutation(s): 0 
EC: 2.1.1.73
UniProt
Find proteins for P05102 (Haemophilus parahaemolyticus)
Explore P05102 
Go to UniProtKB:  P05102
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05102
Sequence Annotations
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains LengthOrganismImage
5'-D(P*GP*TP*CP*AP*GP*CP*GP*CP*AP*TP*GP*G)-3'A [auth C]12N/A
Sequence Annotations
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains LengthOrganismImage
5'-D(P*CP*CP*AP*TP*GP*AP*GP*CP*TP*GP*AP*C)-3'B [auth D]12N/A
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SAH
Query on SAH
Download Ideal Coordinates CCD File 
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: 2.87 Å
  • R-Value Work: 0.156 
  • R-Value Observed: 0.156 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.86α = 90
b = 99.86β = 90
c = 325.2γ = 120
Software Package:
Software NamePurpose
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-11-30
    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