Motor Proteins in DNA Metabolism: Structures and Mechanisms


Major processes of DNA metabolism such as replication, recombination and repair, require mechanical, vectorial translocation of enzymes along the nucleic acid. Enzymes involved in these processes, particularly helicases and polymerases, must possess motor protein capabilities to be able to perform their functions.

Keywords: motor proteins; protein machines; DNA metabolism; polymerases; helicases

Figure 1.

Schematic, heuristic model of a protein motor performing vectorial translocation along the ssDNA. The protein has two effective DNA‐binding sites, s1 and s2. The protein also has structural and functional asymmetry. The enzyme–DNA complex goes through a cycle of different conformational and binding states in response to the binding of NTP (black circle), its hydrolysis, and release of the NTP hydrolysis product (grey circle). The NTP hydrolysis is coupled to the protein structure changes synchronized with the changes of the affinities of the ssDNA‐binding sites. As a result, with each cycle of NTP binding and hydrolysis, the protein performs unidirectional translocation on the DNA lattice.

Figure 2.

An outline of the active, rolling model of the DNA unwinding and mechanical translocation proposed for the Escherichia coli Rep helicase. In the presence of ATP, the Rep dimer, associated with the 3′ ssDNA arm of the DNA fork, acquires functional and structural asymmetry, with one subunit having a high affinity for the ss and the other for the dsDNA conformation. As a result, the dimer invades the duplex part of the fork. Unwinding and hydrolysis of ATP returns the protein–DNA complex to the initial state, but with a different subunit now engaged in interactions with the ssDNA. The reaction results in net translocation of the Rep dimer on the ssDNA in the 3′ → 5′ direction (Lohman and Bjornson, ).

Figure 3.

Current model of the Escherichia coli DnaB hexamer bound to a replication fork DNA substrate. The hexamer, bound to the 5′ arm of the fork, is oriented towards the dsDNA with the large domain of each protomer as the ssDNA passes through the cross channel. The ATP binding sites (black circles) are adjacent to the strong ssDNA‐binding subsite that is near the small 12 kDa domain of each protomer (Jezewska et al., ). The arrow indicates the direction of the helicase translocation.

Figure 4.

Schematic representation of a DNA polymerase, based on the structure of the Escherichia coli pol I Klenow fragment, in the complex with template‐primer DNA (Joyce and Steitz, ).



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Further Reading

Alberts B and Miyake‐Lye R (1992) Unscrambling the puzzle of biological machines: the importance of the details. Cell 68: 415–420.

Baker TA and Bell SP (1998) Polymerases and the replisome: machines within machines. Cell 92: 295–305.

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Lohman TM, Thorn K and Vale RD (1998) Staying on track: common features of DNA helicases and microtubule motors. Cell 93: 9–12.

Marians KJ (1999) PriA at the crossroads of DNA replication and recombination. Progress in Nucleic Acid Research and Molecular Biology 63: 39–67.

Matson SW and Kaiser‐Rogers KA (1990) DNA helicases. Annual Review of Biochemistry 59: 289–329.

San Martin MC, Stamford NPJ, Dammerova N, Dixon NE and Carazo JM (1995) A structural model for the Escherichia coli DnaB helicase based on electron microscopy data. Journal of Structural Biology 114: 167–176.

Stillman B (1994) Smart machines at the DNA replication fork. Cell 78: 725–728.

Young MC, Kuhl SB and von Hippel PH (1994) Kinetic theory of ATP‐driven translocases on one‐dimensional polymer lattices. Journal of Molecular Biology 235: 1436–1446.

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Bujalowski, Wlodzimierz(Apr 2001) Motor Proteins in DNA Metabolism: Structures and Mechanisms. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1038/npg.els.0003561]