PDBsum entry 2f03

Hydrolase/DNA

PDB id: 2f03

Contents

Protein chains

269 a.a.

DNA/RNA

Metals

_CA ×2

Waters ×111

PDB id:

2f03

Name:

Hydrolase/DNA

Title:

Crystal structure of tetrameric restriction endonuclease sfii in complex with cognate DNA (partial bound form)

Structure:

DNA (5'- d( Ap Tp G Tp Gp Gp Cp Cp Ap Ap Cp Ap Ap Gp Gp Cp Cp Tp Ap Tp T)-3'). Chain: e, g. Engineered: yes. DNA (5'- d( Ap Ap Tp Ap Gp Gp Cp Cp Tp Tp Gp Tp Tp Gp Gp Cp Cp Ap Cp Ap T)- 3'). Chain: f, h. Engineered: yes.

Source:

Synthetic: yes. Other_details: e.Coli

Resolution:

3.05Å R-factor: 0.241 R-free: 0.293

Ensemble:

2 models

Authors:

A.K.Aggarwal,E.S.Vanamee,H.Viadiu

Key ref:

E.S.Vanamee et al. (2005). A view of consecutive binding events from structures of tetrameric endonuclease SfiI bound to DNA. EMBO J, 24, 4198-4208. PubMed id: 16308566 DOI: 10.1038/sj.emboj.7600880

Date:

11-Nov-05 Release date: 16-Jan-07

Protein chains

O52512  (T2S1_STRFI) -  Type II restriction enzyme SfiI from Streptomyces fimbriatus

Seq: 269 a.a.

Struc: 269 a.a.

DNA/RNA chains

T-G-G-C-C-A-A-C 8 bases

T-T-G-G-C-C-A 7 bases

T-G-G-C-C 5 bases

G-G-C-C-A 5 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: 10.1038/sj.emboj.7600880

EMBO J 24:4198-4208 (2005)

PubMed id: 16308566

A view of consecutive binding events from structures of tetrameric endonuclease SfiI bound to DNA.

E.S.Vanamee, H.Viadiu, R.Kucera, L.Dorner, S.Picone, I.Schildkraut, A.K.Aggarwal.

ABSTRACT

Many reactions in cells proceed via the sequestration of two DNA molecules in a synaptic complex. SfiI is a member of a growing family of restriction enzymes that can bind and cleave two DNA sites simultaneously. We present here the structures of tetrameric SfiI in complex with cognate DNA. The structures reveal two different binding states of SfiI: one with both DNA-binding sites fully occupied and the other with fully and partially occupied sites. These two states provide details on how SfiI recognizes and cleaves its target DNA sites, and gives insight into sequential binding events. The SfiI recognition sequence (GGCCNNNN[downward arrow]NGGCC) is a subset of the recognition sequence of BglI (GCCNNNN[downward arrow]NGGC), and both enzymes cleave their target DNAs to leave 3-base 3' overhangs. We show that even though SfiI is a tetramer and BglI is a dimer, and there is little sequence similarity between the two enzymes, their modes of DNA recognition are unusually similar.

Selected figure(s)

Figure 5.
Figure 5 Change in loop E conformation. (A) Loop E enters the DNA major groove in the native complex (blue), but in the C/D dimer of the Se-Met complex (red) it packs away from the DNA. Black spheres mark the position of Arg 213. (B) View of C/D dimer looking down the DNA axis. In the native complex (blue), loop E's bracket the DNA and help to hold it in place, while in the Se-Met complex (red) the loops are positioned away from the DNA.

Figure 6.
Figure 6 The active sites of SfiI (left) and BglI (right). The DNA and the active site residues of SfiI (Asp 79, Asp100, and Lys102) and BglI (Asp116, Asp142, and Lys144) are shown in 'stick' representation. The scissile phosphodiester is indicated by arrows. The Ca^2+ ions are shown as nonbonded spheres and colored aqua, water molecules are not shown. In SfiI, the second Ca^2+ is missing and the scissile phosphodiester is 3 Å further away than in BglI, indicating that the enzyme is in an inactive state.

The above figures are reprinted by permission from Macmillan Publishers Ltd: EMBO J (2005, 24, 4198-4208) copyright 2005.

Figures were selected by an automated process.