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PDBsum entry 1dc1

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protein dna_rna ligands Protein-protein interface(s) links
Hydrolase/DNA PDB id
1dc1
Jmol
Contents
Protein chains
310 a.a.
DNA/RNA
Ligands
DIO ×10
Waters ×474
PDB id:
1dc1
Name: Hydrolase/DNA
Title: Restriction enzyme bsobi/DNA complex structure: encirclement of the DNA and histidine-catalyzed hydrolysis within a canonical restriction enzyme fold
Structure: DNA (5'-d( T Ap Tp Ap Cp Tp Cp Gp Ap Gp Tp Ap T)- 3'). Chain: w, c. Engineered: yes. Bsobi restriction endonuclease. Chain: a, b. Synonym: type ii restriction enzyme, type ii site specific deoxyribonuclease. Engineered: yes
Source: Synthetic: yes. Other_details: DNA sequence designed for crystallization based on the central recognition sequence of bacillus stearothermophilus. Geobacillus stearothermophilus. Organism_taxid: 1422. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Tetramer (from PQS)
Resolution:
1.70Å     R-factor:   0.190     R-free:   0.253
Authors: M.J.Van Der Woerd,J.J.Pelletier,S.-Y.Xu,A.M.Friedman
Key ref:
M.J.van der Woerd et al. (2001). Restriction enzyme BsoBI-DNA complex: a tunnel for recognition of degenerate DNA sequences and potential histidine catalysis. Structure, 9, 133-144. PubMed id: 11250198 DOI: 10.1016/S0969-2126(01)00564-0
Date:
04-Nov-99     Release date:   21-Feb-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P70985  (T2B1_GEOSE) -  Type-2 restriction enzyme BsoBI
Seq:
Struc:
323 a.a.
310 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.3.1.21.4  - Type Ii site-specific deoxyribonuclease.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates.
      Cofactor: Mg(2+)
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     nucleic acid phosphodiester bond hydrolysis   3 terms 
  Biochemical function     hydrolase activity     6 terms  

 

 
DOI no: 10.1016/S0969-2126(01)00564-0 Structure 9:133-144 (2001)
PubMed id: 11250198  
 
 
Restriction enzyme BsoBI-DNA complex: a tunnel for recognition of degenerate DNA sequences and potential histidine catalysis.
M.J.van der Woerd, J.J.Pelletier, S.Xu, A.M.Friedman.
 
  ABSTRACT  
 
BACKGROUND: 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. RESULTS: 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. CONCLUSIONS: 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.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Overall Structure of the BsoBI-DNA Complex(a) The BsoBI-DNA complex viewed along the DNA helical axis. The protein monomers (chain A, yellow; chain B, blue) are shown encircling the DNA strands (green). The scissile phosphates are marked with the large black sphere, and the noncrystallographic 2-fold is oriented vertically.(b) A stereo a carbon diagram detailing a view of the BsoBI-DNA complex rotated vert, similar 90 about the vertical from (a) so that the DNA axis now runs horizontally. Every tenth residue is marked by a small black sphere and many are numbered.(c) Molecular surface of the BsoBI dimer, demonstrating the close opposition and complete enclosure of DNA in the tunnel. The orientation is the same as (a). One scissile phosphate (black sphere) is visible.(d) A stereo pair of the molecular surface in the same orientation as (b)

 
  The above figure is reprinted by permission from Cell Press: Structure (2001, 9, 133-144) copyright 2001.  
  Figure was selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19747545 P.Zhang, P.H.Too, J.C.Samuelson, S.H.Chan, T.Vincze, S.Doucette, S.Bäckström, K.D.Potamousis, T.M.Schramm, D.Forrest, D.C.Schwartz, and S.Y.Xu (2010).
Engineering BspQI nicking enzymes and application of N.BspQI in DNA labeling and production of single-strand DNA.
  Protein Expr Purif, 69, 226-234.  
18456708 J.Orlowski, and J.M.Bujnicki (2008).
Structural and evolutionary classification of Type II restriction enzymes based on theoretical and experimental analyses.
  Nucleic Acids Res, 36, 3552-3569.  
17584917 L.Knizewski, L.N.Kinch, N.V.Grishin, L.Rychlewski, and K.Ginalski (2007).
Realm of PD-(D/E)XK nuclease superfamily revisited: detection of novel families with modified transitive meta profile searches.
  BMC Struct Biol, 7, 40.  
17567609 Y.Zheng, and R.J.Roberts (2007).
Selection of restriction endonucleases using artificial cells.
  Nucleic Acids Res, 35, e83.  
16628220 M.Bochtler, R.H.Szczepanowski, G.Tamulaitis, S.Grazulis, H.Czapinska, E.Manakova, and V.Siksnys (2006).
Nucleotide flips determine the specificity of the Ecl18kI restriction endonuclease.
  EMBO J, 25, 2219-2229.
PDB codes: 2fqz 2gb7
15590682 H.Hashimoto, T.Shimizu, T.Imasaki, M.Kato, N.Shichijo, K.Kita, and M.Sato (2005).
Crystal structures of type II restriction endonuclease EcoO109I and its complex with cognate DNA.
  J Biol Chem, 280, 5605-5610.
PDB codes: 1wtd 1wte
16195548 Q.S.Xu, R.J.Roberts, and H.C.Guo (2005).
Two crystal forms of the restriction enzyme MspI-DNA complex show the same novel structure.
  Protein Sci, 14, 2590-2600.
PDB code: 1yfi
15893669 S.A.Townson, J.C.Samuelson, S.Y.Xu, and A.K.Aggarwal (2005).
Implications for switching restriction enzyme specificities from the structure of BstYI bound to a BglII DNA sequence.
  Structure, 13, 791-801.
PDB codes: 1vrr 1yuv
15805123 Z.Yang, J.R.Horton, R.Maunus, G.G.Wilson, R.J.Roberts, and X.Cheng (2005).
Structure of HinP1I endonuclease reveals a striking similarity to the monomeric restriction enzyme MspI.
  Nucleic Acids Res, 33, 1892-1901.
PDB code: 1ynm
12142452 M.Fuxreiter, and I.Simon (2002).
Protein stability indicates divergent evolution of PD-(D/E)XK type II restriction endonucleases.
  Protein Sci, 11, 1978-1983.  
12124289 S.J.Koch, A.Shundrovsky, B.C.Jantzen, and M.D.Wang (2002).
Probing protein-DNA interactions by unzipping a single DNA double helix.
  Biophys J, 83, 1098-1105.  
11557805 A.Pingoud, and A.Jeltsch (2001).
Structure and function of type II restriction endonucleases.
  Nucleic Acids Res, 29, 3705-3727.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.