PDBsum entry 1b8h

Transferase

PDB id: 1b8h

Contents

Protein chains

228 a.a. *

11 a.a. *

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Building a replisome from interacting pieces: sliding clamp complexed to a peptide from DNA polymerase and a polymerase editing complex.

Authors

Y.Shamoo, T.A.Steitz.

Ref.

Cell, 1999, 99, 155-166. [DOI no: 10.1016/S0092-8674(00)81647-5]

PubMed id

10535734

Abstract

We have solved the crystal structures of the bacteriophage RB69 sliding clamp, its complex with a peptide essential for DNA polymerase interactions, and the DNA polymerase complexed with primer-template DNA. The editing complex structure shows a partially melted duplex DNA exiting from the exonuclease domain at an unexpected angle and significant changes in the protein structure. The clamp complex shows the C-terminal 11 residues of polymerase bound in a hydrophobic pocket, and it allows docking of the editing and clamp structures together. The peptide binds to the sliding clamp at a position identical to that of a replication inhibitor peptide bound to PCNA, suggesting that the replication inhibitor protein p21CIP1 functions by competing with eukaryotic polymerases for the same binding pocket on the clamp.

Figure 3.
Figure 3. Peptide Interactions with the Sliding ClampThe interaction of pol-CT with RB69 sliding clamp is close fitting and consists mainly of hydrophobic interactions. Accessible surface of RB69 sliding clamp is shown in blue, while pol-CT is displayed as a stick model. To illustrate the pol-CT-binding pocket, all the sliding clamp surfaces within 4.5 Å of the pol-CT model are colored in yellow. The figure was made using GRASP ([37]).

Figure 4.
Figure 4. Residues of the T4 and RB69 Pol-CTs that Are Similar to the ClampResidues in the RB69 pol-CT that are colored in blue are different in the T4 pol-CT. Residues that are the same in T4 and RB69 are shown in red. Residues that differ point away from the pol-CT-binding pocket (Table 1).

The above figures are reprinted by permission from Cell Press: Cell (1999, 99, 155-166) copyright 1999.