PDBsum entry 2fdc

DNA binding protein/DNA

PDB id: 2fdc

Contents

Protein chains

505 a.a. *

585 a.a. *

DNA/RNA

Ligands

FLQ

* Residue conservation analysis

PDB id:

2fdc

Name:

DNA binding protein/DNA

Title:

Structural basis of DNA damage recognition and processing by uvrb: crystal structure of a uvrb/DNA complex

Structure:

5'-d(p Cp Gp Gp Cp Tp Cp Cp Ap Tp Cp Tp Cp Tp Ap Cp Cp Gp C p Ap A)-3'. Chain: c, d. Engineered: yes. Uvrabc system protein b. Chain: a, b. Synonym: uvrb protein, excinuclease abc subunit b. Engineered: yes

Source:

Synthetic: yes. Bacillus caldotenax. Organism_taxid: 1395. Gene: uvrb. Expressed in: escherichia coli. Expression_system_taxid: 562

Biol. unit:

Dimer (from PQS)

Resolution:

3.30Å R-factor: 0.210 R-free: 0.258

Authors:

J.J.Truglio,C.Kisker

Key ref:

J.J.Truglio et al. (2006). Structural basis for DNA recognition and processing by UvrB. Nat Struct Mol Biol, 13, 360-364. PubMed id: 16532007 DOI: 10.1038/nsmb1072

Date:

13-Dec-05 Release date: 14-Mar-06

Protein chain

P56981  (UVRB_BACCA) -  UvrABC system protein B from Bacillus caldotenax

Seq: 658 a.a.

Struc: 505 a.a.

Protein chain

P56981  (UVRB_BACCA) -  UvrABC system protein B from Bacillus caldotenax

Seq: 658 a.a.

Struc: 585 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

DNA/RNA chains

C-G-G-C-T-T-A-C-C-G-C-A 12 bases

C-C-G-C-A 5 bases

Enzyme reactions

• Enzyme class: Chains A, B: E.C.?

DOI no: 10.1038/nsmb1072

Nat Struct Mol Biol 13:360-364 (2006)

PubMed id: 16532007

Structural basis for DNA recognition and processing by UvrB.

J.J.Truglio, E.Karakas, B.Rhau, H.Wang, M.J.DellaVecchia, B.Van Houten, C.Kisker.

ABSTRACT

DNA-damage recognition in the nucleotide excision repair (NER) cascade is a complex process, operating on a wide variety of damages. UvrB is the central component in prokaryotic NER, directly involved in DNA-damage recognition and guiding the DNA through repair synthesis. We report the first structure of a UvrB-double-stranded DNA complex, providing insights into the mechanism by which UvrB binds DNA, leading to formation of the preincision complex. One DNA strand, containing a 3' overhang, threads behind a beta-hairpin motif of UvrB, indicating that this motif inserts between the strands of the double helix, thereby locking down either the damaged or undamaged strand. The nucleotide directly behind the beta-hairpin is flipped out and inserted into a small, highly conserved pocket in UvrB.

Selected figure(s)

Figure 1.
Figure 1. The UvrB–DNA complex and selected electron density. (a) Surface of UvrB is color-coded by domain (yellow, 1a; green, 1b; blue, 2; red, 3; cyan, the -hairpin of UvrB; magenta, the newly formed -sheet after DNA binding). DNA is illustrated by spokes and letters, color-coded by nucleotide type. The letter representation of the DNA is in a similar orientation to the DNA in the structure. Black letters, disordered nucleotides; F, fluorescein-adducted thymine. The fluorescein-dT, although partially ordered (Fig. 1b), has been omitted from the figure for clarity. (b) 2F[o] - F[c] electron density map contoured at 1.0 covering the DNA. Gray, carbons of unmodified nucleotides; green, carbons of partially ordered fluorescein; magenta, electron density for the fluorescein. Nucleotides are labeled consecutively from 5' to 3', omitting numbers of disordered residues. (c) UvrB–DNA model showing how the inner strand of the DNA (red) travels between the -hairpin (cyan) and domain 1b and the outer strand (green) travels around the outside of the -hairpin. (d) Superposition of DNA-bound and apo UvrB. -hairpin regions of the DNA-bound (cyan and blue) and apo UvrB (PDB entry 1D9X; yellow and gold) are superimposed. Select residues are shown with color-coded labeling. Dark gray spokes represent the bound DNA and the surface of the remainder of the UvrB–DNA complex is shown in gray.

Figure 2.
Figure 2. Interactions between UvrB and the DNA. (a) UvrB bound to DNA. Gray surface, UvrB; cyan ribbon, -hairpin; yellow, outer DNA strand; green, inner DNA strand. Selected residues from UvrB are indicated. 3' and 5' ends of the DNA are labeled in red. Nucleotides are numbered sequentially starting from the 5' end and omitting numbers corresponding to nucleotides in the loop region. (b,c) Views rotated 45° (b) and 90° (c) from a along the vertical axis.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Mol Biol (2006, 13, 360-364) copyright 2006.