PDBsum entry 2d7d

Hydrolase/DNA

PDB id: 2d7d

Contents

Protein chains

621 a.a.

38 a.a.

DNA/RNA

Ligands

ADP

Waters ×204

References listed in PDB file

Key reference

Title

Structural insights into the cryptic DNA-Dependent atpase activity of uvrb.

Authors

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

Ref.

J Mol Biol, 2006, 357, 62-72. [DOI no: 10.1016/j.jmb.2005.12.059]

PubMed id

16426634

Abstract

The UvrABC pathway is a ubiquitously occurring mechanism targeted towards the repair of bulky base damage. Key to this process is UvrB, a DNA-dependent limited helicase that acts as a lesion recognition element whilst part of a tracking complex involving UvrA, and as a DNA-binding platform required for the presentation of damage to UvrC for subsequent processing. We have been able to determine the structure of a ternary complex involving UvrB* (a C-terminal truncation of full-length UvrB), a polythymine trinucleotide and ADP. This structure has highlighted the roles of key conserved residues in DNA binding distinct from those of the beta-hairpin, where most of the attention in previous studies has been focussed. We are also the first to report the structural basis underlying conformational re-modelling of the beta-hairpin that is absolutely required for DNA binding and how this event results in an ATPase primed for catalysis. Our data provide the first insights at the molecular level into the transformation of UvrB into an active helicase.

Figure 2.
Figure 2. (a) The 2F[o] -F[c] omit map contoured at 1s for the trithymine oligonucleotide. (b) Protein-DNA interactions. The trinucleotide binds at the entrance to a channel in the interface between the b-hairpin loop and residues comprising domains 1a and 1b. The majority of contacts involve hydrogen bonds between the phosphate groups of the thymine nucleotides (5'-T1 to T3-3') and residues Thr481 in domain 3, Lys67 in domain 1a, Ser 91 at the N terminus of the b-hairpin loop and Ser141 (also in domain 1a). The furanose sugar and base of T3 stack against the aryl moieties of Tyr146 and Tyr96, respectively.

Figure 6.
Figure 6. The relative positions of a modelled g-phosphate group, DEAD/H box (yellow), Lys67 together with its near environment (red) and tyrosine residues that form the base of the b-hairpin (magenta). These elements are all favourably juxtaposed for the transduction of signals between the ATP and DNA-binding sites.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2006, 357, 62-72) copyright 2006.

Secondary reference #1

Title

Structural insights into the cryptic DNA-Dependent atpase activity of uvrb.

Authors

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

Ref.

J Mol Biol, 2006, 357, 62-72. [DOI no: 10.1016/j.jmb.2005.12.059]

PubMed id

16426634

Note: In the PDB file this reference is annotated as "TO BE PUBLISHED". The citation details given above have been manually determined.

Figure 2.
Figure 2. (a) The 2F[o] -F[c] omit map contoured at 1s for the trithymine oligonucleotide. (b) Protein-DNA interactions. The trinucleotide binds at the entrance to a channel in the interface between the b-hairpin loop and residues comprising domains 1a and 1b. The majority of contacts involve hydrogen bonds between the phosphate groups of the thymine nucleotides (5'-T1 to T3-3') and residues Thr481 in domain 3, Lys67 in domain 1a, Ser 91 at the N terminus of the b-hairpin loop and Ser141 (also in domain 1a). The furanose sugar and base of T3 stack against the aryl moieties of Tyr146 and Tyr96, respectively.

Figure 6.
Figure 6. The relative positions of a modelled g-phosphate group, DEAD/H box (yellow), Lys67 together with its near environment (red) and tyrosine residues that form the base of the b-hairpin (magenta). These elements are all favourably juxtaposed for the transduction of signals between the ATP and DNA-binding sites.

The above figures are reproduced from the cited reference with permission from Elsevier