DNA modification-dependent restriction endonuclease AspBHI

Experimental Data Snapshot

  • Resolution: 2.88 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 

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Structure and mutagenesis of the DNA modification-dependent restriction endonuclease AspBHI.

Horton, J.R.Nugent, R.L.Li, A.Mabuchi, M.Y.Fomenkov, A.Cohen-Karni, D.Griggs, R.M.Zhang, X.Wilson, G.G.Zheng, Y.Xu, S.Y.Cheng, X.

(2014) Sci Rep 4: 4246-4246

  • DOI: https://doi.org/10.1038/srep04246
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The modification-dependent restriction endonuclease AspBHI recognizes 5-methylcytosine (5mC) in the double-strand DNA sequence context of (C/T)(C/G)(5mC)N(C/G) (N = any nucleotide) and cleaves the two strands a fixed distance (N12/N16) 3' to the modified cytosine. We determined the crystal structure of the homo-tetrameric AspBHI. Each subunit of the protein comprises two domains: an N-terminal DNA-recognition domain and a C-terminal DNA cleavage domain. The N-terminal domain is structurally similar to the eukaryotic SET and RING-associated (SRA) domain, which is known to bind to a hemi-methylated CpG dinucleotide. The C-terminal domain is structurally similar to classic Type II restriction enzymes and contains the endonuclease catalytic-site motif of DX20EAK. To understand how specific amino acids affect AspBHI recognition preference, we generated a homology model of the AspBHI-DNA complex, and probed the importance of individual amino acids by mutagenesis. Ser41 and Arg42 are predicted to be located in the DNA minor groove 5' to the modified cytosine. Substitution of Ser41 with alanine (S41A) and cysteine (S41C) resulted in mutants with altered cleavage activity. All 19 Arg42 variants resulted in loss of endonuclease activity.

  • Organizational Affiliation

    Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, Georgia 30322, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
restriction endonuclease AspBHI
A, B, C, D
388Azoarcus oleariusMutation(s): 0 
Gene Names: azo0355
Find proteins for A1K2B7 (Azoarcus sp. (strain BH72))
Explore A1K2B7 
Go to UniProtKB:  A1K2B7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA1K2B7
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.88 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 
  • Space Group: P 62
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 195.092α = 90
b = 195.092β = 90
c = 81.45γ = 120
Software Package:
Software NamePurpose
SERGUIdata collection
PHENIXmodel building
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 2014-03-19 
  • Deposition Author(s): Horton, J.R.

Revision History  (Full details and data files)

  • Version 1.0: 2014-03-19
    Type: Initial release