PDBsum entry 2p0j

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protein dna_rna Protein-protein interface(s) links
Hydrolase/DNA PDB id
Protein chains
203 a.a.
Waters ×334
PDB id:
Name: Hydrolase/DNA
Title: Structure of restriction endonuclease bstyi bound to non-cog
Structure: 5'-d( Ap Tp Gp Ap Ap Tp Cp Cp Ap Tp A)-3'. Chain: c. Engineered: yes. 5'-d( Tp Ap Tp Gp Gp Ap Tp Tp Cp Ap T)-3'. Chain: d. Engineered: yes. Bstyi. Chain: a, b. Engineered: yes
Source: Synthetic: yes. Geobacillus stearothermophilus. Organism_taxid: 1422. Gene: bstyir. Expressed in: escherichia coli. Expression_system_taxid: 562.
2.10Å     R-factor:   0.199     R-free:   0.239
Authors: S.A.Townson,J.C.Samuelson,Y.Bao,S.Y.Xu,A.K.Aggarwal
Key ref:
S.A.Townson et al. (2007). BstYI Bound to Noncognate DNA Reveals a "Hemispecific" Complex: Implications for DNA Scanning. Structure, 15, 449-459. PubMed id: 17437717 DOI: 10.1016/j.str.2007.03.002
28-Feb-07     Release date:   01-May-07    
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   2 terms 
  Biochemical function     DNA binding     3 terms  


DOI no: 10.1016/j.str.2007.03.002 Structure 15:449-459 (2007)
PubMed id: 17437717  
BstYI Bound to Noncognate DNA Reveals a "Hemispecific" Complex: Implications for DNA Scanning.
S.A.Townson, J.C.Samuelson, Y.Bao, S.Y.Xu, A.K.Aggarwal.
DNA recognition by proteins is essential for specific expression of genes in a living organism. En route to a target DNA site, a protein will often sample noncognate DNA sites through nonspecific protein-DNA interactions, resulting in a variety of conformationally different binding states. We present here the crystal structure of endonuclease BstYI bound to a noncognate DNA. Surprisingly, the structure reveals the enzyme in a "hemispecific" binding state on the pathway between nonspecific and specific recognition. A single base pair change in the DNA abolishes binding of only one monomer, with the second monomer bound specifically. We show that the enzyme binds essentially as a rigid body, and that one end of the DNA is accommodated loosely in the binding cleft while the other end is held tightly. Another intriguing feature of the structure is Ser172, which has a dual role in establishing nonspecific and specific contacts. Taken together, the structure provides a snapshot of an enzyme in a "paused" intermediate state that may be part of a more general mechanism of scanning DNA.
  Selected figure(s)  
Figure 1.
Figure 1. Structure of the BstYI Hemispecific Complex; Comparison with Free and Specific
View looking down the DNA axis. The left-hand (L) and right-hand (R) monomers are highlighted in light blue (left) and red (right), respectively; DNA duplexes are colored yellow, and the mutated base pair is highlighted in cyan. In the hemispecific complex, the R monomer makes base-specific contacts to the unmutated DNA half-site, as in the specific complex. In contrast, all base-specific contacts are lost to the mutated DNA half-site, and there is a distinct cavity between the DNA major groove and the L monomer.
Figure 3.
Figure 3. DNA Recognition
(A–C) Close-up view (left) and schematic representation (right) of DNA contacts in the (A) fully specific complex, the (B) hemispecific cognate half-site, and the (C) noncognate half-site. The DNA-recognition sequences are highlighted in yellow, and the mutated base pair is highlighted in cyan. Hydrogen bonding is indicated with dashed, red lines (left), and with solid, red or black lines for base-specific and phosphate contacts, respectively (right). DNA recognition in the cognate half-site is almost identical to that in the fully specific complex, with Ser172 and Lys133 mediating the base-specific contacts. However, in the hemispecific structure, the Lys133 contact is direct and not water mediated, and there is a loss of some phosphate contacts. In contrast, a single base change in the noncognate half-site abolishes any contacts to the bases, and there are only a handful of contacts to the phosphate backbone, including one from the recognition residue S172.
  The above figures are reprinted by permission from Cell Press: Structure (2007, 15, 449-459) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20375284 I.E.Sánchez, D.U.Ferreiro, M.Dellarole, and Prat-Gay (2010).
Experimental snapshots of a protein-DNA binding landscape.
  Proc Natl Acad Sci U S A, 107, 7751-7756.  
19380375 M.Sokolowska, H.Czapinska, and M.Bochtler (2009).
Crystal structure of the beta beta alpha-Me type II restriction endonuclease Hpy99I with target DNA.
  Nucleic Acids Res, 37, 3799-3810.
PDB codes: 3fc3 3gox
19905543 O.Bénichou, Y.Kafri, M.Sheinman, and R.Voituriez (2009).
Searching fast for a target on DNA without falling to traps.
  Phys Rev Lett, 103, 138102.  
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
18534978 F.W.Perrino, Silva, S.Harvey, E.E.Pryor, D.W.Cole, and T.Hollis (2008).
Cooperative DNA binding and communication across the dimer interface in the TREX2 3' --> 5'-exonuclease.
  J Biol Chem, 283, 21441-21452.  
17437711 A.Pingoud, and W.Wende (2007).
A sliding restriction enzyme pauses.
  Structure, 15, 391-393.  
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.