E. coli DNA Polymerase III
Beta Subunit:
The Sliding DNA Clamp

David Marcey
© 2021

I. Introduction
II. Monomer and Dimer Structure
III. Interactions with DNA
IV. References


Please leave comments/suggestions or please acknowledge use of this site by visiting our feedback page

[Back to OMM Exhibits]

This exhibit displays molecules in the left part of the screen, and text that addresses structure-function relationships of the molecules in the right part (below). Use the scrollbar to the right to scroll through the text. If you are using browser other than Firefox (the recommended browser for this site), be sure to allow popups. In Chrome, you can click on the popup blocker icon in the right part of the address bar..

To evoke renderings of the molecule that illustrate particular points, click the radio buttons:

Please click the load PDB buttons, , when present.

To reset the molecule, use the reset buttons:

If you are a practiced user, you can create the illusion of 3D if you turn on stereo mode. In this mode, when you train one eye on one image and the other eye on the other image, you will elicit a centered image that appears truly 3-dimensional. To turn on stereo mode when viewing a scene, return here and use this button . To turn off stereo mode, return here and use this button .

To view a Pol III Beta molecule in AR (augmented reality) on your phone or notebook, see the directions on the OMM exhibit page and then use your camera to scan this image:

I. Introduction

The remarkable, donut-shaped molecule to your left is the beta subunit of DNA polymerase III of E. coli (pol III). This subunit provides for the remarkable processivity of the holoenzyme during DNA replication. Processivity refers to ability of polymerases to add many hundreds or thousands of nucleotides to a growing chain without dissociating from the template. Processivity partially accounts for the rapid rates of DNA synthesis by DNA polymerases. For example, E. coli replicates its entire genome in ~40 minutes (~80,000 bp/min). The pol III beta subunit is a ring-shaped clamp that embraces DNA in a central 35 angstrom hole, tethering the remainder of pol III to the template.

return to beginning of the exhibit

II. Monomer and Dimer Structure

The beta subunit is a homodimer of two, 366 amino acid monomers, each monomer providing one half of the clamp.

The dimer interface is a novel continuation, across the monomer boundary, of a beta sheet structure, indistinguishable from intra-monomer beta sheets (one interface is illustrated here). In addition to four strong hydrogen bonds that link the beta strands across the interface, there are several other linkages helping to stabilize the dimer, including:

hydrophobic interactions of amino acid sidechains - R groups of phe106 and ile108 of one monomer pack against ile272 and leu273 of the other and form a hydrophobic core;

ionic bonds (salt bridges) between four pairs of amino acid side chains exposed to solvent (water);

ionic bond pairs (arg96-glu300 and arg103-glu304) that are inaccessible to solvent and that likely form particularly strong ionic bonds.

The beta subunit monomers are arranged in a head-to-tail (N-C-->N-C-->) orientation. This produces non-symmetric faces of the dimeric ring.

The two carboxy termini project from the face that binds the remainder of the Pol III holoenzyme. Note that this face contains prominent loops that are well-suited to bind other pol III subunits.

Each monomer comprises three domains with nearly identical structure, but not identical amino acid sequence. The amino, central, and carboxy domains each harbor an outer layer of two beta sheets that support 2 inner alpha helices. Thus, the core of the dimeric clamp is lined with 12 alpha helices (2 helices/domain x 3 domains/monomer x 2 monomers).


return to beginning of exhibit

III. Interaction with DNA

The 35 Angstrom hole of the beta dimer is large enough to accommodate double helical nucleic acid with little steric hindrance as modeled here for B-DNA (~20 Angstrom diameter). The tilt of the 12 central alpha helices is similar due to the symmetrical arrangement of the six domains. The axis of each alpha helix can be seen to be perpendicular to the sugar-phosphate backbone of both major and minor DNA grooves when the DNA is modeled perpendicular to the plane of the beta clamp ring. Many DNA-binding proteins contain alpha helices that are oriented parallel to the nucleic acid backbone. This orientation allows the alpha helices to recognize and fit into the major groove of target DNA. In contrast, the perpendicular orientation of the beta clamp helices and DNA backbone seems designed to prevent access of the protein to either DNA groove and therefore to facilitate rapid sliding of the clamp along the DNA axis.

These principles hold for interaction with A-form DNA-RNA duplexes (~25 Angstrom diameter), found at the site of initial clamping of the Beta subunit at the RNA-primed template of the start of an Okazaki fragment.


return to beginning of exhibit

IV. References

Kong, X-P., Onrust, R., O'Donnell, M., and J. Kuriyan (1992). Three-Dimensional Structure of the Beta Subunit of E. coli DNA Polymerase III Holoenzyme: A Sliding DNA Clamp. Cell 69: 425-437.


return to beginning of exhibit