7LNJ

CamA Adenine Methyltransferase Complexed to Cognate Substrate DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.68 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Clostridioides difficile specific DNA adenine methyltransferase CamA squeezes and flips adenine out of DNA helix.

Zhou, J.Horton, J.R.Blumenthal, R.M.Zhang, X.Cheng, X.

(2021) Nat Commun 12: 3436-3436

  • DOI: https://doi.org/10.1038/s41467-021-23693-w
  • Primary Citation of Related Structures:  
    7LNI, 7LNJ, 7LT5

  • PubMed Abstract: 

    Clostridioides difficile infections are an urgent medical problem. The newly discovered C. difficile adenine methyltransferase A (CamA) is specified by all C. difficile genomes sequenced to date (>300), but is rare among other bacteria. CamA is an orphan methyltransferase, unassociated with a restriction endonuclease. CamA-mediated methylation at CAAAAA is required for normal sporulation, biofilm formation, and intestinal colonization by C. difficile. We characterized CamA kinetic parameters, and determined its structure bound to DNA containing the recognition sequence. CamA contains an N-terminal domain for catalyzing methyl transfer, and a C-terminal DNA recognition domain. Major and minor groove DNA contacts in the recognition site involve base-specific hydrogen bonds, van der Waals contacts and the Watson-Crick pairing of a rearranged A:T base pair. These provide sufficient sequence discrimination to ensure high specificity. Finally, the surprisingly weak binding of the methyl donor S-adenosyl-L-methionine (SAM) might provide avenues for inhibiting CamA activity using SAM analogs.


  • Organizational Affiliation

    Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX, USA.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Site-specific DNA-methyltransferase (adenine-specific)
A, B, C
578Clostridioides difficile 630Mutation(s): 0 
Gene Names: CD630_27580
EC: 2.1.1.72
UniProt
Find proteins for Q183J3 (Clostridioides difficile (strain 630))
Explore Q183J3 
Go to UniProtKB:  Q183J3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ183J3
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA Strand 2D [auth E],
G,
I
14synthetic construct
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA Strand 1E [auth D],
F,
H
14synthetic construct
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.68 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.253α = 90
b = 161.361β = 90
c = 230.633γ = 90
Software Package:
Software NamePurpose
SERGUIdata collection
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM049245-23

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-19
    Type: Initial release
  • Version 1.1: 2021-07-14
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Database references, Refinement description