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PDB:2POL

Protein Name

E. coli DNA polymerase III, beta-subunit

Species

Escherichia coli (bacteria)

Biological Context

DNA replication is a process required in all organisms before any of its cells divides into daughter cells. DNA replication involves the accurate duplication of the vast amounts of genetic information encoded in the DNA. It requires the splitting of the double stranded parent DNA into two single strands, unwinding of the parent strands and creation of two new strands using the two parent strands as templates. DNA polymerases are enzymes that play an important role in DNA duplication. DNA polymerases exist in two types - processive ones, which function during cell division and perform rapid replication of very long stretches of DNA without dissociating from the template, and non-processive ones, which normally function during DNA repair and operate on shorter stretches of the template. The E. coli Pol (polymerase) III holoenzyme is a complex made up of at least 10 different protein subunits. The core polymerase consists of alpha, epsilon and delta subunits. The beta subunit is transferred to the core polymerase by the gamma subunit. The beta subunit lends processivity to the core polymerase and, once bound, cannot be easily separated from the DNA.

Structure Description

2pol2pol_x2pol_y

The reason for this becomes clear from its structure shown here. The beta subunit of E.coli has the structure of a closed star-shaped ring (diameter 80 Angstroms) with a hole (diameter about 35 Angstroms) in the middle which is large enough to accommodate either the A or B forms of DNA (diameter about 25 Angstroms) without any steric repulsion. (Fig.1). It is a dimer with each monomer having three similar domains consisting of an outer layer of two beta sheets and an inner layer of two alpha helices. As a result the beta subunit forms a rigid molecule with an inner surface of 12 helices surrounded by an outer surface of six beta sheets. The structure is highly symmetric and hence well suited to interact with the cylindrically symmetric DNA duplex. Though the outer surface has a high negative charge, the inner surface of the ring has a positive charge which probably stabilizes the dimer around DNA. This subunit is structurally similar to the PCNA protein from humans.

1 (Fig.1) The structure of the beta-subunit

Beta-subunit is a homodimer. The diameter of it's center channel is ~35Å.
This is large enough to let dsDNA(diameter : ~25Å) through.

Protein Data Bank (PDB)

References

Source

Kong, X.P. Onrust, R. O'Donnell, M. Kuriyan, J.; "Three-dimensional structure of the beta subunit of E. coli DNA polymerase III holoenzyme: a sliding DNA clamp."; Cell; (1992) 69:425-437 PubMed:1349852.

Others

UniProt:P00583

author: Ashwini Patil


Japanese version:PDB:2POL