RSS

PDB:3BEP

Protein Name

E. coli DNA polymerase III, beta-subunit / DNA complex

Species

Escherichia coli

Biological Context

The genetic information which is the fundamental of organism is coded as base sequence in the double-stranded DNA(dsDNA). DNA replication is the process of copying massive genetic information accurately and conserved in all organisms including bacteria, eucaryote and virus. This process must happen before cell division. At the beginning, a dsDNA are separated into two single-stranded DNA(ssDNA) at specific locations(called origin) in the genome. This cleave structure is called replication bubble and has two Y-shaped replication forks. Next, the two replication forks proceed in both directions, with synthesizing new ssDNA strands. A number of proteins are involved in this phase. (refer to Fig.1 for DNA synthesis of E.coli). As a result, a parental dsDNA is replicated to two daughter dsDNAs. And each daughter dsDNA is distributed to each daughter cell. (refer to PDB:2IUU about distribution of DNA into daughter ascell of E.coli).

(Fig.1) DNA synthesis at a replication fork(in case of E.coli)
Two new dsDNAs are created by using the two parent ssDNAs as templates near the replication fork.

STEP1:
DnaB helicase(blue) separates a dsDNA into two ssDNAs, as cutting the hydrogen bands between base pairs. It seems to as if unzip.
Topoisomerase(lime green) has a role in rewinding the twist of double helices which was generated by the dsDNA separation.

STEP2:
The separated ssDNA has a tendency of annealing. For preventing annealing,
Single-Stranded DNA Binding Protein : SSB(brown) bind to separated ssDNA.

STEP3:
DnaG primase(purple) is activated by binding to DnaB helicase,
and synthesizes a short RNA primer approximately 10 nucleotides long using a ssDNA as a template.

STEP4:
DNA polymerase III elongates a new ssDNA strand by adding a deoxyribonucleotide at a time
in the 5'-3' direction to the RNA primer, using a ssDNA as a template.
The E.coli polymerase III is a complex consisting of multiple different protein subunits.
The core part(green) consists of three subunits(alpha, epsilon, delta). The clamp part is beta subunit(navy blue),
and clamp-loader part is gamma complex(yellow).

It is the core part(alpha, epsilon, delta) that performs a practical function of the DNA synthesis in the E.coli DNA polymerase III. The beta subunit works as a clamp preventing the core part from dissociating from the DNA and it is equipped to the core part by the gamma complex which works as a clamp loader. These proteins are different among species. (refer to Table.1).

(Table.1) E.coli T4 Virus Yeast
DNA Polymerase Pol III core(α,ε,θ) gp43 Pol α, Pol δ, Pol ε
Clamp Pol III β-subunit gp45 PCNA
Clamp loader Pol III γ-complex gp44/62 RFC

The clamp crystal structure of E.coli(PDB:2POL), T4 virus(xPSSS:1CZD), and yeast(PDB:1SXJ) have been determined. (refer to Fig.2). Each of them has a ring shape polymer with a channel(diameter : about 35 Angstroms) in the center which is large enough to accommodate a dsDNA. However, a clamp bound to DNA has not been directly observed. It remains unclear how the clamp slides on the DNA. Therefore, the crystal structure of the E. coli beta-clamp bound to dsDNA was determined here.

2
(Fig.2) Three kinds of the clamp structure

Structure Description

3bep3bep_x3bep_y

The beta-subunit of E.coli has the structure of a closed ring (diameter 80 Angstroms) with a hole (diameter about 35 Angstroms). The hole is large enough to accommodate either the A or B forms of DNA (diameter about 25 Angstroms without any steric repulsion. 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. The structure is highly symmetric and hence well suited to interact with the cylindrically symmetric DNA duplex. The newly-determined complex structure of Beta-clamp and dsDNA showed that dsDNA goes through the b-clamp at a steep angle(approximately 22 degree). (Fig.3 right). Two residues(R24 and Q149) are exposed from each protomer of the C-terminal face, the face to which pol III core and clamp loader bind. In the complex structure described here, dsDNA interacts with the two residues from protmer B. (Fig.3 left). However, If dsDNA lean to the other side at approximately 22 degree, it may interacts with the two residues from protomer A.

3
(Fig.3) The complexed structure of beta-clamp and dsDNA

Beta-clamp is a homodimer and thus has two identical protein binding sites, through with it can bind two different proteins at once. (Fig.4).

4
(Fig.4) The two protein binding sites of the Beta-clamp

From these results, it can be speculated that beta-clamp facilitate switching of the DNA between two different DNA polymerases bound to the same beta-clamp. (Fig.5).

5
(Fig.5) DNA switching

Furthermore, the experiments conducted by Roxana and et al showed that the ssDNA can directly binds to the protein binding site of the beta-clamp. This specific interaction may act as a "placeholder" to hold the clamp at the primed site after Pol III core dissociates from the beta-clamp. (Fig.6).

6
(Fig.6) Play a role as a placeholder

Protein Data Bank (PDB)

References

Source

Georgescu, R.E. Kim, S.S. Yurieva, O. Kuriyan, J. Kong, X.-P. O'Donnell, M.; "Structure of a sliding clamp on DNA"; Cell(Cambridge,Mass.); (2008) 132:43-54 PubMed:18191219.

Others

author: Jun-ichi Ito


Japanese version:PDB:3BEP