PDBsum entry 2nmv

Hydrolase/DNA

PDB id: 2nmv

Contents

Protein chains

620 a.a. *

38 a.a. *

DNA/RNA

Ligands

NML

FLU

ADP

* Residue conservation analysis

PDB id:

2nmv

Name:

Hydrolase/DNA

Title:

Damage detection by the uvrabc pathway: crystal structure of uvrb bound to fluorescein-adducted DNA

Structure:

5'-d(p Tp Tp Tp Tp T)-3'. Chain: d. Engineered: yes. Uvrabc system protein b. Chain: a. Synonym: protein uvrb, excinuclease abc subunit b, protein dina. Engineered: yes. Uvrabc system protein b. Chain: b.

Source:

Synthetic: yes. Bacillus subtilis. Organism_taxid: 1423. Gene: uvrb. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.95Å R-factor: 0.227 R-free: 0.281

Authors:

T.R.Waters,J.Eryilmaz,S.Geddes,T.E.Barrett

Key ref:

T.R.Waters et al. (2006). Damage detection by the UvrABC pathway: Crystal structure of UvrB bound to fluorescein-adducted DNA. FEBS Lett, 580, 6423-6427. PubMed id: 17097086 DOI: 10.1016/j.febslet.2006.10.051

Date:

23-Oct-06 Release date: 16-Jan-07

Protein chain

P37954  (UVRB_BACSU) -  UvrABC system protein B from Bacillus subtilis (strain 168)

Seq: 661 a.a.

Struc: 620 a.a.

Protein chain

P37954  (UVRB_BACSU) -  UvrABC system protein B from Bacillus subtilis (strain 168)

Seq: 661 a.a.

Struc: 38 a.a.

DNA/RNA chain

T-T-T-T-T 5 bases

Enzyme reactions

• Enzyme class: Chains A, B: E.C.3.1.-.-

DOI no: 10.1016/j.febslet.2006.10.051

FEBS Lett 580:6423-6427 (2006)

PubMed id: 17097086

Damage detection by the UvrABC pathway: Crystal structure of UvrB bound to fluorescein-adducted DNA.

T.R.Waters, J.Eryilmaz, S.Geddes, T.E.Barrett.

ABSTRACT

UvrB is the damage recognition element of the highly conserved UvrABC pathway that functions in the removal of bulky DNA adducts. Pivotal to this is the formation of a damage detection complex that relies on the ability of UvrB to locate and sequester diverse lesions. Whilst structures of UvrB bound to DNA have recently been reported, none address the issue of lesion recognition. Here, we describe the crystal structure of UvrB bound to a pentanucleotide containing a single fluorescein-adducted thymine that reveals a unique mechanism for damage detection entirely dependent on the exclusion of lesions larger than an undamaged nucleotide.

Selected figure(s)

Figure 1.
Fig. 1. (A) The molecular structure of T-fluorescein. (B) An overview of the UvrB molecule (represented as a molecular surface) showing the relative locations of the pentathymine molecule (cyan), the conserved β-hairpin (light green), domains 1a (yellow), 1b (grey), 2 (green) and 3 (pink). (C) A magnified view of the pentathymine molecule identifying the position of the T-fluorescein adducted nucleotide, TF3 (magenta), together with associated F[o] − F[c] omit map density contoured at 2.5σ. The location of the lesion reveals that the damage is extruded away from the UvrB molecule. PT5 denotes the 5′ phosphate group of T5 that is the only visible moiety of this nucleotide. All figures were generated using Pymol (Delano Scientific, www.pymol.org).

Figure 2.
Fig. 2. Superposition of the pentathymine (light blue), trithymine (yellow) and stem–loop (grey) UvrB–DNA complexes. The fluorescein triple ring systems within the stem loop and pentathymine structures are shown in orange and magenta respectively.

The above figures are reprinted by permission from the Federation of European Biochemical Societies: FEBS Lett (2006, 580, 6423-6427) copyright 2006.

Figures were selected by an automated process.