crystal structure of M1.HpyAVI-SAM complex

Experimental Data Snapshot

  • Resolution: 3.10 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.223 

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Biochemical and structural characterization of a DNA N6-adenine methyltransferase from Helicobacter pylori

Ma, B.Ma, J.Liu, D.Guo, L.Chen, H.Ding, J.Liu, W.Zhang, H.

(2016) Oncotarget 7: 40965-40977

  • DOI: https://doi.org/10.18632/oncotarget.9692
  • Primary Citation of Related Structures:  
    5HEK, 5HFJ

  • PubMed Abstract: 

    DNA N6-methyladenine modification plays an important role in regulating a variety of biological functions in bacteria. However, the mechanism of sequence-specific recognition in N6-methyladenine modification remains elusive. M1.HpyAVI, a DNA N6-adenine methyltransferase from Helicobacter pylori, shows more promiscuous substrate specificity than other enzymes. Here, we present the crystal structures of cofactor-free and AdoMet-bound structures of this enzyme, which were determined at resolutions of 3.0 Å and 3.1 Å, respectively. The core structure of M1.HpyAVI resembles the canonical AdoMet-dependent MTase fold, while the putative DNA binding regions considerably differ from those of the other MTases, which may account for the substrate promiscuity of this enzyme. Site-directed mutagenesis experiments identified residues D29 and E216 as crucial amino acids for cofactor binding and the methyl transfer activity of the enzyme, while P41, located in a highly flexible loop, playing a determinant role for substrate specificity. Taken together, our data revealed the structural basis underlying DNA N6-adenine methyltransferase substrate promiscuity.

  • Organizational Affiliation

    Department of Human Anatomy, Histology and Embryology, Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education, and State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, Beijing, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Adenine specific DNA methyltransferase (DpnA)
A, B, C, D, E
A, B, C, D, E, F, G, H
232Helicobacter pylori 26695Mutation(s): 0 
Gene Names: HP_0050
Find proteins for O24891 (Helicobacter pylori (strain ATCC 700392 / 26695))
Explore O24891 
Go to UniProtKB:  O24891
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO24891
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.10 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.223 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 135.603α = 90
b = 135.603β = 90
c = 265.146γ = 120
Software Package:
Software NamePurpose
XDSmodel building

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-11-16
    Type: Initial release
  • Version 1.1: 2016-11-30
    Changes: Database references
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Refinement description