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595 a.a.
_ZN
Key reference
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 coresheet (
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 CThe 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.
Literature references that cite this PDB file's key reference
PubMed id Reference
19287003 D.Pakotiprapha, Y.Liu, G.L.Verdine, and D.Jeruzalmi (2009).
A Structural Model for the Damage-sensing Complex in Bacterial Nucleotide Excision Repair.J Biol Chem, 284, 12837-12844.
PDB code: 3fpn
19700770 M.N.Murphy, P.Gong, K.Ralto, L.Manelyte, N.J.Savery, and K.Theis (2009).
An N-terminal clamp restrains the motor domains of the bacterial transcription-repair coupling factor Mfd.Nucleic Acids Res, 37, 6042-6053.
PDB code: 3hjh
19183285 M.Pruteanu, and T.A.Baker (2009).
Controlled degradation by ClpXP protease tunes the levels of the excision repair protein UvrA to the extent of DNA damage.Mol Microbiol, 71, 912-924.
19458048 M.T.Sung, Y.T.Lai, C.Y.Huang, L.Y.Chou, H.W.Shih, W.C.Cheng, C.H.Wong, and C.Ma (2009).
Crystal structure of the membrane-bound bifunctional transglycosylase PBP1b from Escherichia coli.Proc Natl Acad Sci U S A, 106, 8824-8829.
PDB codes: 3fwl 3fwm
18996898 L.A.Christensen, H.Wang, B.Van Houten, and K.M.Vasquez (2008).
Efficient processing of TFO-directed psoralen DNA interstrand crosslinks by the UvrABC nuclease.Nucleic Acids Res, 36, 7136-7145.
16829526 D.L.Croteau, M.J.DellaVecchia, H.Wang, R.J.Bienstock, M.A.Melton, and B.Van Houten (2006).
The C-terminal zinc finger of UvrA does not bind DNA directly but regulates damage-specific DNA binding.J Biol Chem, 281, 26370-26381.
16595666 H.Wang, M.J.DellaVecchia, M.Skorvaga, D.L.Croteau, D.A.Erie, and B.Van Houten (2006).
UvrB domain 4, an autoinhibitory gate for regulation of DNA binding and ATPase activity.J Biol Chem, 281, 15227-15237.
16532007 J.J.Truglio, E.Karakas, B.Rhau, H.Wang, M.J.DellaVecchia, B.Van Houten, and C.Kisker (2006).
Structural basis for DNA recognition and processing by UvrB.Nat Struct Mol Biol, 13, 360-364.
PDB code: 2fdc
15308661 M.J.DellaVecchia, D.L.Croteau, M.Skorvaga, S.V.Dezhurov, O.I.Lavrik, and B.Van Houten (2004).
Analyzing the handoff of DNA from UvrA to UvrB utilizing DNA-protein photoaffinity labeling.J Biol Chem, 279, 45245-45256.
15456749 M.Skorvaga, M.J.DellaVecchia, D.L.Croteau, K.Theis, J.J.Truglio, B.S.Mandavilli, C.Kisker, and B.Van Houten (2004).
Identification of residues within UvrB that are important for efficient DNA binding and damage processing.J Biol Chem, 279, 51574-51580. The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.
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