3D Structure of Transposase

CPK Color Scheme

On this page, you can see a monomer of transposase complexed with the 19bp DNA recognition sequence. A complete transposase complex consists of two monomers of transposase and two 19bp DNA recognition sequences. For the complete complex visit the Protein Data Bank.

Reset and spin the transposase complex.

Notice the 19bp DNA recognition sequence (in green) and the transposase secondary structure. Alpha helices are in purple and beta sheets are in white. The monomer begins with the amino acid alanine (red) and ends with glycine (orange).

View the different domains of transposase. The N-terminal domain is in pale blue. The C-terminal domain is in tan. The catalytic domain is in orange. Even though transposase can be divided into domains, each domain's function is not exclusive. All three domains participate in every function of transposase. The DNA is in green.

Look closer at the catalytic domain. Notice the active site DDE motif and its proximity to the DNA (green). Asp97 is in white. Asp188 is in gray. Glu326 is in violet. The DDE motif is found throughout transposases and species.

Now find the divalent metal ion, Mn2+ (yellow), used to help catalyze the DNA nicking and backbone reforming. Where is it in relation to the DDE motif?

Identify the basic trench. Where is the DNA in relation to this trench? This trench helps to hold the DNA and create an environment suitable for nucleophilic attacks. It consists of 16 amino acids (in gray) with basic side chains.

Special thanks to...

Dr. A. Malcolm Campbell for providing templates and Jmol tutorials.

Nathan Silva and David Marcey for An Introduction to Jmol Scripting.

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