PDBsum entry 1tc3

DNA binding protein/DNA

PDB id: 1tc3

Contents

Protein chain

51 a.a.

DNA/RNA

Waters ×49

PDB id:

1tc3

Name:

DNA binding protein/DNA

Title:

Transposase tc3a1-65 from caenorhabditis elegans

Structure:

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

Source:

Synthetic: yes. Caenorhabditis elegans. Organism_taxid: 6239. Strain: bergerac. Variant: tr679. Organelle: nucleus. Gene: tc3a. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Hexamer (from PDB file)

Resolution:

2.45Å R-factor: 0.234 R-free: 0.318

Authors:

G.Van Pouderoyen,R.F.Ketting,A.Perrakis,R.H.A.Plasterk,T.K.Sixma

Key ref:

G.van Pouderoyen et al. (1997). Crystal structure of the specific DNA-binding domain of Tc3 transposase of C.elegans in complex with transposon DNA. EMBO J, 16, 6044-6054. PubMed id: 9312061 DOI: 10.1093/emboj/16.19.6044

Date:

07-Jul-97 Release date: 21-Nov-97

Protein chain

P34257  (TC3A_CAEEL) -  Transposable element Tc3 transposase from Caenorhabditis elegans

Seq: 329 a.a.

Struc: 51 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

DNA/RNA chains

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

A-G-T-T-C-T-A-T-A-G-G-A-C-C-C-C-C-C-C-T 20 bases

DOI no: 10.1093/emboj/16.19.6044

EMBO J 16:6044-6054 (1997)

PubMed id: 9312061

Crystal structure of the specific DNA-binding domain of Tc3 transposase of C.elegans in complex with transposon DNA.

G.van Pouderoyen, R.F.Ketting, A.Perrakis, R.H.Plasterk, T.K.Sixma.

ABSTRACT

The crystal structure of the complex between the N-terminal DNA-binding domain of Tc3 transposase and an oligomer of transposon DNA has been determined. The specific DNA-binding domain contains three alpha-helices, of which two form a helix-turn-helix (HTH) motif. The recognition of transposon DNA by the transposase is mediated through base-specific contacts and complementarity between protein and sequence-dependent deformations of the DNA. The HTH motif makes four base-specific contacts with the major groove, and the N-terminus makes three base-specific contacts with the minor groove. The DNA oligomer adopts a non-linear B-DNA conformation, made possible by a stretch of seven G:C base pairs at one end and a TATA sequence towards the other end. Extensive contacts (seven salt bridges and 16 hydrogen bonds) of the protein with the DNA backbone allow the protein to probe and recognize the sequence-dependent DNA deformation. The DNA-binding domain forms a dimer in the crystals. Each monomer binds a separate transposon end, implying that the dimer plays a role in synapsis, necessary for the simultaneous cleavage of both transposon termini.

Selected figure(s)

Figure 2.
Figure 2 Protein -DNA contacts. (A) A schematic view with ribbons drawn through the C s of the Tc3A DNA-binding domain (yellow) and through the phosphate backbone of the DNA strands (blue and magenta). (B) Sketch summarizing the hydrogen bonding (indicated by green dotted lines, base-specific H-bonds by green solid lines) and salt bridging contacts (blue lines) between the Tc3A domain and the DNA. Gray boxes indicate residues involved in base-specific contacts. Hydrogen bonds are at a maximum distance of 3.5 Å and salt bridges at a maximum of 4.0 Å (Barlow and Thorton, 1983). (C) and (D) Stereo views (Kraulis, 1991) of the HTH DNA contacts in the major groove, and the N-terminus of Tc3A bound in the minor groove of DNA, respectively. Hydrogen bonds are indicated with green dotted lines.

Figure 4.
Figure 4 The Tc3A domain bound to DNA. The protein is shown in an electrostatic surface representation with positively and negatively charged regions in blue and red respectively (GRASP-scale -10 to +10). DNA is shown in stick representation, with carbons in white, nitrogens in blue, oxygens in red and phosphors in yellow.

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (1997, 16, 6044-6054) copyright 1997.

Figures were selected by the author.