PDBsum entry 1t5l

DNA excision repair

PDB id: 1t5l

Contents

Protein chains

595 a.a. *

Metals

_ZN ×4

Waters ×196

* Residue conservation analysis

PDB id:

1t5l

Name:

DNA excision repair

Title:

Crystal structure of the DNA repair protein uvrb point mutant y96a revealing a novel fold for domain 2

Structure:

Uvrabc system protein b. Chain: a, b. Synonym: uvrb protein, excinuclease abc subunit b. Engineered: yes. Mutation: yes

Source:

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

Resolution:

2.60Å R-factor: 0.233 R-free: 0.287

Authors:

J.J.Truglio,D.L.Croteau,M.Skorvaga,M.J.Dellavecchia,K.Theis, B.S.Mandavilli,B.Van Houten,C.Kisker

Key ref:

J.J.Truglio et al. (2004). Interactions between UvrA and UvrB: the role of UvrB's domain 2 in nucleotide excision repair. EMBO J, 23, 2498-2509. PubMed id: 15192705 DOI: 10.1038/sj.emboj.7600263

Date:

04-May-04 Release date: 22-Jun-04

Protein chains

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

Seq: 658 a.a.

Struc: 595 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1038/sj.emboj.7600263

EMBO J 23:2498-2509 (2004)

PubMed id: 15192705

Interactions between UvrA and UvrB: the role of UvrB's domain 2 in nucleotide excision repair.

J.J.Truglio, D.L.Croteau, M.Skorvaga, M.J.DellaVecchia, K.Theis, B.S.Mandavilli, B.Van Houten, C.Kisker.

ABSTRACT

Nucleotide excision repair (NER) is a highly conserved DNA repair mechanism present in all kingdoms of life. UvrB is a central component of the bacterial NER system, participating in damage recognition, strand excision and repair synthesis. None of the three presently available crystal structures of UvrB has defined the structure of domain 2, which is critical for the interaction with UvrA. We have solved the crystal structure of the UvrB Y96A variant, which reveals a new fold for domain 2 and identifies highly conserved residues located on its surface. These residues are restricted to the face of UvrB important for DNA binding and may be critical for the interaction of UvrB with UvrA. We have mutated these residues to study their role in the incision reaction, formation of the pre-incision complex, destabilization of short duplex regions in DNA, binding to UvrA and ATP hydrolysis. Based on the structural and biochemical data, we conclude that domain 2 is required for a productive UvrA-UvrB interaction, which is a pre-requisite for all subsequent steps in nucleotide excision repair.

Selected figure(s)

Figure 1.
Figure 1 Three-dimensional structure of the UvrA-interacting domain (domain 2) of UvrB. The ribbon diagram shows the secondary structure elements and mutated residues on the proposed UvrA interacting face. The core sheet ( 2 - 7) is shown in green, a second sheet in blue ( 1, 8) and the single helix in pink. Blue spheres as well as residue labels mark the beginning and end of domain 2.

Figure 3.
Figure 3 Comparison of the Y96A UvrB structure to WT UvrB. (A) Stereo view of the interface between domain 2 and the remainder of the UvrB molecule. Selected side chains are shown and labeled. Color coding is according to domain architecture as in Figure 2A and domain 2 in blue. Hydrogen bonds and salt bridges are indicated by red dotted lines. (B) Comparison of the overall structure of WT UvrB (cyan) and the two NCS-related copies of UvrB Y96A (yellow and red) as a stereo view. Orientation is chosen as in Figure 2. For the superposition, domain 1a of each of the structures was used and the resulting transformations were applied to the entire molecule. (C) Superposition of UvrB Y96A (color coded as in Figure 2) and WT UvrB (gray). Side chains for Tyr 92, Asp 117 and Arg 190 are shown for both the WT and the UvrB Y96A structure. The side chain of Y96 is omitted from the native model since the electron density for this residue is insufficient. A sphere indicates the position of the C atom of Y96 (A96 for the mutant).

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2004, 23, 2498-2509) copyright 2004.

Figures were selected by the author.