PDBsum entry 1d9z

Gene regulation

PDB id: 1d9z

Contents

Protein chain

590 a.a. *

Ligands

ATP

Metals

_MG

_ZN ×2

* Residue conservation analysis

PDB id:

1d9z

Name:

Gene regulation

Title:

Crystal structure of the DNA repair protein uvrb in complex with atp

Structure:

Excinuclease uvrabc component uvrb. Chain: a. Engineered: yes

Source:

Bacillus caldotenax. Organism_taxid: 1395. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

3.15Å R-factor: 0.262 R-free: 0.335

Authors:

K.Theis,P.J.Chen,M.Skorvaga,B.Van Houten,C.Kisker

Key ref:

K.Theis et al. (1999). Crystal structure of UvrB, a DNA helicase adapted for nucleotide excision repair. EMBO J, 18, 6899-6907. PubMed id: 10601012 DOI: 10.1093/emboj/18.24.6899

Date:

30-Oct-99 Release date: 03-May-00

Protein chain

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

Seq: 658 a.a.

Struc: 590 a.a.

DOI no: 10.1093/emboj/18.24.6899

EMBO J 18:6899-6907 (1999)

PubMed id: 10601012

Crystal structure of UvrB, a DNA helicase adapted for nucleotide excision repair.

K.Theis, P.J.Chen, M.Skorvaga, B.Van Houten, C.Kisker.

ABSTRACT

Nucleotide excision repair (NER) is a highly conserved DNA repair mechanism. NER systems recognize the damaged DNA strand, cleave it on both sides of the lesion, remove and newly synthesize the fragment. UvrB is a central component of the bacterial NER system participating in damage recognition, strand excision and repair synthesis. We have solved the crystal structure of UvrB in the apo and the ATP-bound forms. UvrB contains two domains related in structure to helicases, and two additional domains unique to repair proteins. The structure contains all elements of an intact helicase, and is evidence that UvrB utilizes ATP hydrolysis to move along the DNA to probe for damage. The location of conserved residues and structural comparisons allow us to predict the path of the DNA and suggest that the tight pre-incision complex of UvrB and the damaged DNA is formed by insertion of a flexible beta-hairpin between the two DNA strands.

Selected figure(s)

Figure 2.
Figure 2 The ATP binding site. Residues in the vicinity of the ATP are shown in an all-bonds representation. The ATP molecule is shown as a ball-and-stick model and the Mg2+ ion is indicated by a sphere; hydrogen bonds are shown as dotted lines.

Figure 3.
Figure 3 Conserved residues and electrostatic potential on the surface of UvrB. For a better view into the ATP binding site, domain 3 has been rotated by 120° away from the remainder of UvrB to show the interface between domains 1a and 3. The ATP molecule has been duplicated in the figure, shown in its orientation with respect to domains 1a and 3. Residues 96 -98 and 109 -113 were omitted from the surface calculation and are shown as a cyan backbone worm for a better view into the cleft between domains 1a and 1b. (A) Side chains on the surface of UvrB that are conserved throughout 16 UvrB sequences are colored according to their location in helicase motifs I-VI. Magenta, motifs I and IV; green, motifs II and V; blue, motifs III and VI; yellow, conserved residues not belonging to any helicase motif. (B) Electrostatic potential calculated separately for domain 3 and for the remainder of the molecule including the bound ATP, at an ionic strength of 0.1 M contoured at 10 k[B]T (k[B] is the Boltzmann constant and T the absolute temperature). Blue, positively charged; red, negatively charged. Figures 3 and 5 were made using GRASP (Nicholls et al., 1991).

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (1999, 18, 6899-6907) copyright 1999.

Figures were selected by an automated process.