DNA‐binding Enzymes: Structural Themes


DNA‐binding enzymes play pivotal roles in nucleic acid biosynthesis. Their structural and functional resemblance bears the imprint of DNA evolution.

Keywords: helicase; polymerase; recombinase; restriction enzyme; topoisomerase

Figure 1.

Model of a DNA replication fork with representative DNA‐binding enzymes in action. An enlarged electron micrograph of a negatively stained hexamer complex of Escherichia coli Rho RNA helicase is shown. ssDBP, single‐stranded DNA‐binding protein. From Knopf KW (1974) PhD thesis, Universität Heidelberg.

Figure 2.

Structure and operation of DNA restriction enzymes. Schemes show the DNA interaction of major ENases as follows. The 440‐kDa multifunctional complex of EcoKI, representative of type I enzymes, acts as a modification methyltransferase on the recognition sequences in which one of the underlined adenine residues is already methylated, or as an ENase on DNA containing unmethylated recognition sequences. DNA binding and recognition of the methylation status is operated by the M/S trimer core complex, to which two R subunits are C‐terminally bound, conferring the ENase function that is encoded by an N‐terminal domain. During DNA restriction both R subunits perform ATP‐dependent DNA translocation followed by single‐strand cleavage, producing random double‐strand breaks in a varying distance and on both sides of the recognition sequence. The 24.6‐kDa ENase of BamHI, a type II enzyme, binds the stated palindromic recognition site in the form of an U‐shaped homodimer complex, and simultaneously cleaves both DNA strands in a sequence specific manner, generating double‐stranded DNA fragments with identically staggered ends. The functional 66.2‐kDa monomer of FokI, a type IIs enzyme, possesses two domains: the N‐terminal DNA recognition domain binds to the recognition site (shaded). The C‐terminal restriction domain, flexibly connected with the N‐terminal domain, is positioned alongside the DNA cleavage signal. The ENase also cleaves hemi‐methylated DNA, is specific but generates double‐stranded DNA fragments with staggered ends of unique sequence composition. EcoP15I, a type III enzyme, is composed of separate restriction (R) and modification (MS) subunits. The latter subunit is required for binding to the stated inversely oriented recognition site (shaded) as well as for its methylation. Cleavage is performed by the R subunit only if the recognition site is unmethylated, and occurs a distance of 25 nucleotides downstream from the recognition signal, resulting in double‐stranded DNA fragments with staggered ends of random sequence composition.

Figure 3.

Model of site specific recombination mechanism by Int family recombinases. Recombinase subunits on different DNA strands are marked in yellow and blue circles, and the conserved catalytic tyrosine (Y) is indicated. Two recombinase subunits bind to each recombination site at inverted repeat sequences that are separated by a short ‘crossover’ region, and synapse the duplex DNA substrates by protein–protein interactions (step I). After the formation of a tetrameric bihelical complex, one strand of each DNA target is cleaved at the 5′ ends of the crossover region forming a covalent 3′ phosphotyrosine intermediate (step II). The freed 5′ ends are exchanged and ligated (step III). During an isomerization event the recombinase dimers dissociate and form a four‐way Holliday junction intermediate (step IV). The Holliday junction is resolved when the second pair of recombinase subunits at the other end of the crossover region carries out the cleavage and strand exchange reaction on the unexchanged strands (steps V and VI).

Figure 4.

Operational modes of topoisomerases of type I and II. A type IB enzyme is shown that binds DNA as a monomer, cleaves and reseals only one strand by forming a covalent 3′‐phosphotyrosine linkage during transient linkage. Type II enzymes bind DNA as a dimer or heterotetramer and perform cleavage and resealing of both strands. Transient cleavage involves two covalent 5′‐phosphotyrosine linkages.



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Further Reading

Viewing enzyme structural models as well as substrate interactions on the molecular level is best achieved by implementing a molecular viewer like RASMOL in the Internet browser. Necessary PDB.files with the molecular data of the enzymes are obtained through links from conventional sequence databanks (Swiss‐Protein Data Library, Gene Bank, Brookhaven Data Bank, Embl Sequence Library). A recommended site containing various model enzymes is: [http://pdb.weizman.ac.il/scop/data/scop.1.005.html]

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DePamphilis ML (1996) DNA Replication in Eukaryotic Cells. CSH Monograph Series vol. 31. Plainview, New York: Cold Spring Harbor Laboratory Press.

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Knopf, Charles W, and Waldeck, Waldemar(Apr 2001) DNA‐binding Enzymes: Structural Themes. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1038/npg.els.0002717]