PDBsum entry 1u3e

DNA binding protein/DNA

PDB id: 1u3e

Contents

Protein chain

174 a.a. *

DNA/RNA

Ligands

EDO ×7

TRS

Metals

_SR ×4

_MN

Waters ×31

* Residue conservation analysis

PDB id:

1u3e

Name:

DNA binding protein/DNA

Title:

DNA binding and cleavage by the hnh homing endonuclease i-hmui

Structure:

36-mer. Chain: a. Engineered: yes. 5'-d( Cp Tp Tp Ap Cp Gp Tp Gp Gp Gp Ap Ap Tp Tp Gp Cp Tp Gp Ap Gp C)-3'. Chain: b. Engineered: yes. 5'-d(p Gp Tp Tp Ap Gp Gp Cp Tp Cp Ap Tp Tp Ap Cp T)-3'. Chain: c.

Source:

Synthetic: yes. Bacillus phage spo1. Organism_taxid: 10685. Gene: bacteriophage sp01. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Tetramer (from PQS)

Resolution:

2.92Å R-factor: 0.216 R-free: 0.247

Authors:

B.W.Shen,M.Landthaler,D.A.Shub,B.L.Stoddard

Key ref:

B.W.Shen et al. (2004). DNA binding and cleavage by the HNH homing endonuclease I-HmuI. J Mol Biol, 342, 43-56. PubMed id: 15313606 DOI: 10.1016/j.jmb.2004.07.032

Date:

21-Jul-04 Release date: 31-Aug-04

Protein chain

P34081  (HMUI_BPSP1) -  DNA endonuclease I-HmuI from Bacillus phage SP01

Seq: 174 a.a.

Struc: 174 a.a.

DNA/RNA chains

G-T-A-A-T-G-A-G-C-C-T-A-A-C-G-C-T-C-A-G-C-A-A-T-T-C-C-C-A-C-G-T-A-A-G-A 36 bases

C-T-T-A-C-G-T-G-G-G-A-A-T-T-G-C-T-G-A-G-C 21 bases

G-T-T-A-G-G-C-T-C-A-T-T-A-C-T 15 bases

Enzyme reactions

• Enzyme class: E.C.3.1.-.-

DOI no: 10.1016/j.jmb.2004.07.032

J Mol Biol 342:43-56 (2004)

PubMed id: 15313606

DNA binding and cleavage by the HNH homing endonuclease I-HmuI.

B.W.Shen, M.Landthaler, D.A.Shub, B.L.Stoddard.

ABSTRACT

The structure of I-HmuI, which represents the last family of homing endonucleases without a defining crystallographic structure, has been determined in complex with its DNA target. A series of diverse protein structural domains and motifs, contacting sequential stretches of nucleotide bases, are distributed along the DNA target. I-HmuI contains an N-terminal domain with a DNA-binding surface found in the I-PpoI homing endonuclease and an associated HNH/N active site found in the bacterial colicins, and a C-terminal DNA-binding domain previously observed in the I-TevI homing endonuclease. The combination and exchange of these features between protein families indicates that the genetic mobility associated with homing endonucleases extends to the level of independent structural domains. I-HmuI provides an unambiguous structural connection between the His-Cys box endonucleases and the bacterial colicins, supporting the hypothesis that these enzymes diverged from a common ancestral nuclease.

Selected figure(s)

Figure 1.
Figure 1. Experimental SAD electron density map used for model building. Left: Map contoured over the entire asymmetric unit. The map is colored according to proximity to the final models of protein (red) and DNA (grey) for clarity. Right: Map contoured at the DNA-protein interface in the region of helices H2 and H3, which connect the HNH core domain and the C-terminal helix-turn-helix DNA binding domain. Residues from these helices interact with base-pairs in the target site minor groove.

Figure 5.
Figure 5. DNA recognition. (a) Superposition of the I-HmuI protein structure (green) with the C-terminal DNA binding domain from the GIY-YIG homing endonuclease I-TevI (light blue). The structure-based alignment of the DNA-binding domains is shown below. The residues involved in DNA contacts in I-HmuI are indicated by black dots. (b) Structure and schematic diagram of the DNA contact regions and residues of I-HmuI. The potential H-bond donors and acceptors, and thymine methyl groups, are indicated as shown in the key. The major groove elements are indicated on the top of the base-pairs; the minor groove elements are indicated on the bottom of the same base-pairs. HNB refers to contacts made by amide nitrogen atoms of the protein backbone. The approximate position where linkers connecting the three main DNA-interacting elements of the protein cross over the DNA phosphate backbone are shown by dotted lines.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2004, 342, 43-56) copyright 2004.

Figures were selected by an automated process.