Escherichia coli DNA topoisomerase I is a 97K enzyme with three domains:  a 67K N-terminal domain responsible for performing the DNA cleavage reaction, a zinc-binding domain which is required for relaxing supercoiled DNA, and a 14K C-terminal DNA-binding domain (Yu, 1995).

    The three dimensional structure for the C-terminal DNA binding domain was determined using heternuclear multidimensional NMR spectroscopy (Yu, 1995).  It consists of two four stranded antiparallel ß-sheets that are seperated by two helices.

A hydrophobic core is formed between one side of the N-terminal ß-sheet (residues V13, L15, L18, F27, L29, V36, and L38) and the helix-loop-helix (residues L57, F60, L68, and L71).   A second hydrophobic core is formed by the C-terminal ß-sheet (V86, V97, W108, Y112, and W117) and two helices (V54 and Y70).   The two helices in the middle of the protein cross at an angle of 123°, which is similar to the interhelical angle observed in the classic helix-turn-helix DNA-binding motif, but the second helix is located in a lower position and is five residues shorter than the DNA-binding motif commonly found (Yu, 1995).  Back to ribbon model .

    The crystal structure was determined for the N-terminal domain at 2.2 Å.  The final model consists of 553 amino acids which is 93% of the polypeptide and 267 water molecules.  The domain is made of four distinct domains which fold and contact each other to generate the shape of an elongated toroid with an overall dimension of 67 Å X 43 Å X 96 Å (Lima, 1994). 

Domain I is made up of four parallel ß-sheets sandwiched between four alpha-helices, two on top and two below.  This structure is similar to an alpha/ß or Rossman fold (Lima, 1994).  Domain II is made up of three antiparallel ß-strands which cross a second set of three antiparallel ß-strands.  The core of domain II is well ordered and filled with mostly aliphatic side chains.  Domain III contains the active site tyrosine and is formed of four helices packing around a central fifth helix.  Domain IV is made up of mostly helical secondary structure.  Four main helices make up this domain upon which several other helices pack including two antiparallel sheets.   A feature of the interaction among the domains is the creation of a large cleft on one side of the protein and a small hole directly adjacent to the large cleft.  The C terminus of the protein is located adjacent to the large cleft which is where it is theorized the C terminal domain fits (Lima, 1994).

Back to Index Page   Back to the description of the tertiary structure of topoisomerase I

Updated:  December 5, 1998

Comments, Questions: luebkeac@uwec.edu