1DC1 | pdb_00001dc1

RESTRICTION ENZYME BSOBI/DNA COMPLEX STRUCTURE: ENCIRCLEMENT OF THE DNA AND HISTIDINE-CATALYZED HYDROLYSIS WITHIN A CANONICAL RESTRICTION ENZYME FOLD

• PDB DOI: https://doi.org/10.2210/pdb1DC1/pdb
• NAKB: 1DC1

• Classification: HYDROLASE/DNA
• Organism(s): Geobacillus stearothermophilus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1999-11-04 Released: 2001-02-21 
• Deposition Author(s): van der Woerd, M.J., Pelletier, J.J., Xu, S.-Y., Friedman, A.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.253 (Depositor) 
• R-Value Work: 
  0.190 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Literature

Restriction enzyme BsoBI-DNA complex: a tunnel for recognition of degenerate DNA sequences and potential histidine catalysis.

van der Woerd, M.J., Pelletier, J.J., Xu, S., Friedman, A.M.

(2001) Structure 9: 133-144

• PubMed: 11250198 
• DOI: https://doi.org/10.1016/s0969-2126(01)00564-0
• Primary Citation Related Structures: 
  1DC1


• PubMed Abstract: 
  

  Restriction endonucleases form a diverse family of proteins with substantial variation in sequence, structure, and interaction with recognition site DNA. BsoBI is a thermophilic restriction endonuclease that exhibits both base-specific and degenerate recognition within the sequence CPyCGPuG. The structure of BsoBI complexed to cognate DNA has been determined to 1.7 A resolution, revealing several unprecedented features. Each BsoBI monomer is formed by inserting a helical domain into an expanded EcoRI-type catalytic domain. DNA is completely encircled by a BsoBI dimer. Recognition sequence DNA lies within a 20 A long tunnel of protein that excludes bulk solvent. Interactions with the specific bases are made in both grooves through direct and water-mediated hydrogen bonding. Interaction with the degenerate position is mediated by a purine-specific hydrogen bond to N7, ensuring specificity, and water-mediated H bonding to the purine N6/O6 and pyrimidine N4/O4, allowing degeneracy. In addition to the conserved active site residues of the DX(n)(E/D)ZK restriction enzyme motif, His253 is positioned to act as a general base. A catalytic mechanism employing His253 and two metal ions is proposed. If confirmed, this would be the first example of histidine-mediated catalysis in a restriction endonuclease. The structure also provides two novel examples of the role of water in protein-DNA interaction. Degenerate recognition may be mediated by employing water as a hydrogen bond donor or acceptor. The structure of DNA in the tunnel may also be influenced by the absence of bulk solvent.

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Organizational Affiliation: 
• Department of Biological Sciences, Purdue University, 47907, West Lafayette, IN, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 82.3 kDa 
• Atom Count: 6,020 
• Modeled Residue Count: 646 
• Deposited Residue Count: 672 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
BSOBI RESTRICTION ENDONUCLEASE	C [auth A], D [auth B]	323	Geobacillus stearothermophilus	Mutation(s): 0  EC: 3.1.21.4
UniProt
Find proteins for P70985 (Geobacillus stearothermophilus) Explore P70985  Go to UniProtKB:  P70985

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*T*AP*TP*AP*CP*TP*CP*GP*AP*GP*TP*AP*T)-3')	A [auth W], B [auth C]	13	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DIO	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth B], K [auth B], L [auth B], M [auth B], N [auth B]	1,4-DIETHYLENE DIOXIDE C4 H8 O2 RYHBNJHYFVUHQT-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.253 (Depositor) 
• R-Value Work:  0.190 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.294	α = 90
b = 87.823	β = 90
c = 99.454	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-02-21 
Deposition Author(s): van der Woerd, M.J., Pelletier, J.J., Xu, S.-Y., Friedman, A.M.

Revision History  

• Version 1.0: 2001-02-21
  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: 2024-02-07
  Changes: Data collection, Database references, Derived calculations