 |
PDBsum entry 1t5l
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
DNA excision repair
|
PDB id
|
|
|
|
1t5l
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
Contents |
 |
|
|
|
|
|
|
|
|
|
|
|
|
* Residue conservation analysis
|
|
|
|
|
References listed in PDB file
|
|
|
Key reference
|
|
|
Title
|
|
Interactions between uvra and uvrb: the role of uvrb'S domain 2 in nucleotide excision repair.
|
|
|
Authors
|
|
J.J.Truglio,
D.L.Croteau,
M.Skorvaga,
M.J.Dellavecchia,
K.Theis,
B.S.Mandavilli,
B.Van houten,
C.Kisker.
|
|
|
Ref.
|
|
EMBO J, 2004,
23,
2498-2509.
[DOI no: ]
|
|
|
PubMed id
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
