PDBsum entry: 1kft

DNA binding protein

PDB-id: 1kft

Contents

Description

Header details

Header records

References

PROCHECK

Protein chain

56 a.a. *

* Residue conservation analysis

Tools

Clefts Calculation

PDB id:

1kft

Name:

DNA binding protein

Title:

Solution structure of thE C-terminal domain of uvrc from e- coli

Structure:

Excinuclease abc subunit c. Chain: a. Fragment: hhh domain(c-terminal domain). Synonym: uvrc. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Strain: de3. Expressed in: escherichia coli. Expression_system_taxid: 562.

UniProt:

P0A8G2 (UVRC_ECO57)

Seq:

Struc:

Seq:

Struc:

Seq:

610 a.a.

Struc:

56 a.a.

Key:	PfamA domain
Secondary structure	CATH domain

Resolution:

not givenÅ

NMR structure:

22 models

Authors:

S.Singh,G.E.Folkers,A.M.J.J.Bonvin,R.Boelens, R.Wechselberger,A.Niztayev,R.Kaptein

Key ref:

S.Singh et al. (2002). Solution structure and DNA-binding properties of the C-terminal domain of UvrC from E.coli.. EMBO J, 21, 6257-6266. [PubMed id: 12426397] [DOI: 10.1093/emboj/cdf627]

Date:

23-Nov-01

Release date:

20-Nov-02

Quick_links

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Clefts

Surface

Key reference

DOI no: 10.1093/emboj/cdf627

EMBO J 21:6257-6266 (2002)

PubMed id: 12426397

Solution structure and DNA-binding properties of the C-terminal domain of UvrC from E.coli.

S.Singh, G.E.Folkers, A.M.Bonvin, R.Boelens, R.Wechselberger, A.Niztayev, R.Kaptein.

ABSTRACT

The C-terminal domain of the UvrC protein (UvrC CTD) is essential for 5' incision in the prokaryotic nucleotide excision repair process. We have determined the three-dimensional structure of the UvrC CTD using heteronuclear NMR techniques. The structure shows two helix-hairpin-helix (HhH) motifs connected by a small connector helix. The UvrC CTD is shown to mediate structure-specific DNA binding. The domain binds to a single-stranded-double-stranded junction DNA, with a strong specificity towards looped duplex DNA that contains at least six unpaired bases per loop ("bubble DNA"). Using chemical shift perturbation experiments, the DNA-binding surface is mapped to the first hairpin region encompassing the conserved glycine-valine-glycine residues followed by lysine-arginine-arginine, a positively charged surface patch and the second hairpin region consisting of glycine-isoleucine-serine. A model for the protein-DNA complex is proposed that accounts for this specificity.

Selected figure(s)

Figure 3.
Figure 3 The NMR solution structure of the UvrC CTD. (A) Backbone stereo view (residues 28−78) of the NMR ensemble (22 structures); the hairpins are coloured in blue. (B) Ribbon view of a representative UvrC CTD structure (closest to average) for residues 23−78. h1 and h2 are the hairpins of HhH motifs. The structures were displayed using the molecular graphics program MOLMOL (Koradi et al., 1996).

Figure 7.
Figure 7 Model representing the interaction of the UvrC CTD with the ds−ss junction. Glycines are coloured red, lysine in blue and threonine in green. This model was obtained by superimposing the two hairpins of UvrC CTD on to the corresponding loops of RNA polymerase II (domain containing the active site of the Rpb1 subunit, PDB accession No. 16IH, see Materials and methods). The structure was generated using the software VMD (Humphrey et al., 1996).

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2002, 21, 6257-6266) copyright 2002.

Figures were selected by an automated process.