4OC8

DNA modification-dependent restriction endonuclease AspBHI


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.884 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

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: 10.1038/srep04246

  • 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 modi ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
restriction endonuclease AspBHI
A, B, C, D
388Azoarcus sp. (strain BH72)N/A
Find proteins for A1K2B7 (Azoarcus sp. (strain BH72))
Go to UniProtKB:  A1K2B7
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B, C, D
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.884 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.197 
  • Space Group: P 62
Unit Cell:
Length (Å)Angle (°)
a = 195.092α = 90.00
b = 195.092β = 90.00
c = 81.450γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHENIXmodel building
PHENIXrefinement
PHENIXphasing
SERGUIdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2014-01-08 
  • Released Date: 2014-03-19 
  • Deposition Author(s): Horton, J.R.

Revision History 

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