PDBsum entry 1vrr

Hydrolase/DNA

PDB id: 1vrr

Contents

Protein chains

203 a.a.

DNA/RNA

Waters ×104

PDB id:

1vrr

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)

Resolution:

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

Date:

02-Jun-05 Release date: 07-Jun-05

Supersedes:

1yuv

Protein chains

Q84AF2  (Q84AF2_GEOSE) -  BstYI from Geobacillus stearothermophilus

Seq: 203 a.a.

Struc: 203 a.a.

DNA/RNA chains

T-T-A-T-A-G-A-T-C-T-A-T-A-A 14 bases

T-T-A-T-A-G-A-T-C-T-A-T-A-A 14 bases

Enzyme reactions

• Enzyme class: E.C.3.1.21.4 - type Ii site-specific deoxyribonuclease.
• Reaction: Endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates.
• Cofactor: Mg(2+)

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.

ABSTRACT

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.