PDBsum entry 1vrr

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protein dna_rna Protein-protein interface(s) links
Hydrolase/DNA PDB id
Jmol PyMol
Protein chains
203 a.a.
Waters ×104
PDB id:
Name: Hydrolase/DNA
Title: Crystal structure of the restriction endonuclease bstyi complex with DNA
Structure: 5'-d( Tp Tp Ap Tp Ap Gp Ap Tp Cp Tp Ap Tp Ap A)- 3'. Chain: c, d. Engineered: yes. Bstyi. Chain: a, b. Engineered: yes. Other_details: type ii restriction endonuclease bstyi
Source: Synthetic: yes. Geobacillus stearothermophilus. Organism_taxid: 1422. Gene: bstyir. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Tetramer (from PQS)
2.70Å     R-factor:   0.230     R-free:   0.267
Authors: S.A.Townson,J.C.Samuelson,S.Y.Xu,A.K.Aggarwal
Key ref:
S.A.Townson et al. (2005). Implications for switching restriction enzyme specificities from the structure of BstYI bound to a BglII DNA sequence. Structure, 13, 791-801. PubMed id: 15893669 DOI: 10.1016/j.str.2005.02.018
02-Jun-05     Release date:   07-Jun-05    
Supersedes: 1yuv
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
Q84AF2  (Q84AF2_GEOSE) -  BstYI
203 a.a.
203 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     DNA restriction-modification system   1 term 
  Biochemical function     Type II site-specific deoxyribonuclease activity     1 term  


DOI no: 10.1016/j.str.2005.02.018 Structure 13:791-801 (2005)
PubMed id: 15893669  
Implications for switching restriction enzyme specificities from the structure of BstYI bound to a BglII DNA sequence.
S.A.Townson, J.C.Samuelson, S.Y.Xu, A.K.Aggarwal.
The type II restriction endonuclease BstYI recognizes the degenerate sequence 5'-RGATCY-3' (where R = A/G and Y = C/T), which overlaps with both BamHI (GGATCC) and BglII (AGATCT), and thus raises the question of whether BstYI DNA recognition will be more BamHI-like or BglII-like. We present here the structure of BstYI bound to a cognate DNA sequence (AGATCT). We find the complex to be more BglII-like with similarities mapping to DNA conformation, domain organization, and residues involved in catalysis. However, BstYI is unique in containing an extended arm subdomain, and the mechanism of DNA capture has both BglII-like and BamHI-like elements. Further, DNA recognition is more minimal than BglII and BamHI, where only two residues mediate recognition of the entire core sequence. Taken together, the structure reveals a mechanism of degenerate DNA recognition and offers insights into the possibilities and limitations in altering specificities of closely related restriction enzymes.
  Selected figure(s)  
Figure 5.
Figure 5. DNA Recognition
(Top) Schematic representation of DNA contacts for BglII (left), BstYI (middle), and BamHI (right). Two-fold symmetry is assumed for all three enzymes. The DNA recognition sequences are highlighted in yellow; with major and minor groove contacts indicated as red and blue lines, respectively. Contacts to the phosphate backbone (purple) are also displayed for BstYI (green). In the BstYI complex, only two residues (Ser172 and Lys133) mediate recognition of the core base pairs and, unlike BamHI and BglII, there is a direct contact to an adenine of a flanking A:T base pair, via Tyr115.
(Bottom) Close-up view of protein-DNA contacts in one half-site of the recognition sequence. DNA bases are colored in yellow and water molecules are colored cyan. Hydrogen bonding is indicated by dashed lines (white). In the BstYI-DNA complex, Ser172 forms a hydrogen bond to the middle cytosine, identical to Asn140 in BglII and Asp154 in BamHI. However, Gly173 does not specify the outer base pair, like the equivalent residues in BglII (Ser141) and BamHI (Arg155). Instead, a cavity between the glycine and the nucleotide allows for water-mediated recognition of N7 of the outer purine by a lysine (Lys133). This lysine residue also forms bidentate hydrogen bonds with the middle guanine and VDW contacts with the inner thymine.
  The above figure is reprinted by permission from Cell Press: Structure (2005, 13, 791-801) copyright 2005.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19567736 R.D.Morgan, and Y.A.Luyten (2009).
Rational engineering of type II restriction endonuclease DNA binding and cleavage specificity.
  Nucleic Acids Res, 37, 5222-5233.  
19081059 E.J.Little, A.C.Babic, and N.C.Horton (2008).
Early interrogation and recognition of DNA sequence by indirect readout.
  Structure, 16, 1828-1837.
PDB code: 3ebc
18400171 G.Tamulaitiene, and V.Siksnys (2008).
NotI is not boring.
  Structure, 16, 497-498.  
17972284 M.Y.Niv, L.Skrabanek, R.J.Roberts, H.A.Scheraga, and H.Weinstein (2008).
Identification of GATC- and CCGG-recognizing Type II REases and their putative specificity-determining positions using Scan2S--a novel motif scan algorithm with optional secondary structure constraints.
  Proteins, 71, 631-640.  
18479503 R.K.Neely, and R.J.Roberts (2008).
The BsaHI restriction-modification system: cloning, sequencing and analysis of conserved motifs.
  BMC Mol Biol, 9, 48.  
17437711 A.Pingoud, and W.Wende (2007).
A sliding restriction enzyme pauses.
  Structure, 15, 391-393.  
17437717 S.A.Townson, J.C.Samuelson, Y.Bao, S.Y.Xu, and A.K.Aggarwal (2007).
BstYI bound to noncognate DNA reveals a "hemispecific" complex: implications for DNA scanning.
  Structure, 15, 449-459.
PDB code: 2p0j
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 code is shown on the right.