PDBsum entry 3bvq

Hydrolase

PDB id: 3bvq

Contents

Protein chains

342 a.a.

Ligands

SO4 ×2

Metals

_FE ×2

PDB id:

3bvq

Name:

Hydrolase

Title:

Crystal structure of apo noti restriction endonuclease

Structure:

Noti restriction endonuclease. Chain: a, b. Engineered: yes

Source:

Nocardia otitidiscaviarum. Organism_taxid: 1823. Gene: notir. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

2.80Å R-factor: 0.266 R-free: 0.335

Authors:

A.R.Lambert,D.Sussman,B.Shen,B.L.Stoddard

Key ref:

A.R.Lambert et al. (2008). Structures of the rare-cutting restriction endonuclease NotI reveal a unique metal binding fold involved in DNA binding. Structure, 16, 558-569. PubMed id: 18400177 DOI: 10.1016/j.str.2008.01.017

Date:

07-Jan-08 Release date: 22-Jan-08

Protein chains

Q2I6W2  (Q2I6W2_9NOCA) -  NotI restriction endonuclease from Nocardia otitidiscaviarum

Seq: 383 a.a.

Struc: 342 a.a.

DOI no: 10.1016/j.str.2008.01.017

Structure 16:558-569 (2008)

PubMed id: 18400177

Structures of the rare-cutting restriction endonuclease NotI reveal a unique metal binding fold involved in DNA binding.

A.R.Lambert, D.Sussman, B.Shen, R.Maunus, J.Nix, J.Samuelson, S.Y.Xu, B.L.Stoddard.

ABSTRACT

The structure of the rare-cutting restriction endonuclease NotI, which recognizes the 8 bp target 5'-GCGGCCGC-3', has been solved with and without bound DNA. Because of its specificity (recognizing a site that occurs once per 65 kb), NotI is used to generate large genomic fragments and to map DNA methylation status. NotI contains a unique metal binding fold, found in a variety of putative endonucleases, occupied by an iron atom coordinated within a tetrahedral Cys4 motif. This domain positions nearby protein elements for DNA recognition, and serves a structural role. While recognition of the central six base pairs of the target is accomplished via a saturated hydrogen bond network typical of restriction enzymes, the most peripheral base pairs are engaged in a single direct contact in the major groove, reflecting reduced pressure to recognize those positions. NotI may represent an evolutionary intermediate between mobile endonucleases (which recognize longer target sites) and canonical restriction endonucleases.

Selected figure(s)

Figure 2.
Figure 2. Homodimeric NotI REase
Domains are colored as described in Figure 1. Select secondary structural elements are numbered for reference. The NotI dimer interface is formed by the domain-swapped α helices (cyan) and the DNA recognition helices (red).

Figure 6.
Figure 6. The NotI Active Site
(A) Active site residues Glu145, Asp160, Glu182, and Gln184 are colored yellow. The bound DNA is colored white, with the scissile phosphate designated orange. The nucleophilic water molecule is shown as a blue sphere and two calcium ions are depicted as magenta spheres. Dashed lines represent interactions between atoms in the active site and numbers indicate distances in angstroms (as average values calculated between the two active sites of the NotI homodimer).
(B) Superposition of active site residues of the P(D)…(D/E)xK active site motif from NotI (green) and BglII (orange). Both REases have a glutamine in the general base position typically occupied by a lysine residue.
(C) Superposition of the two-metal ion active sites of NotI (green) and BamHI (purple). Asp160/Asp94, Glu182/Glu111, and Gln184/Glu113 are residues belonging to the canonical PD…(D/E)xK nuclease motif, while the third acidic residue, Glu145/Glu77, helps coordinate a second metal ion in the active site. The position of this third acidic residue is conserved between the NotI and BamHI enzymes.

The above figures are reprinted from an Open Access publication published by Cell Press: Structure (2008, 16, 558-569) copyright 2008.

Figures were selected by an automated process.