Sandbox Reserved 1260

Heterodimer </scene> alignment.

Specific are highlighted here. The ligands listed above, GDP, Phe, and Mg+2 ion each attach at these locations which are still being explored.

which play a crucial role in binding to the ribosome during translation. They form positive pockets with which negative amino acids can bind to.

'Molecules it Interacts With and where '

The protein binds to GDP as well as the following ligands in order to promote the attachment of the protein complex to the ribosome A site.

PHOSHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER

PHENYLALANINE MAGNESIUM ION

'Origin'

It has domains that are created in yeast (phenyl-transfer RNA) , in the heat resistant Thermus aquaticus (EF-Tu elongation factor, and can be synthetically manufactured.

'Structure'

It has 3 domains. G proteins, Elongation Factors, and the EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain. It is composed of 6 chains, which combine in alignment.

Specific are highlighted here.

which play a crucial role in binding to the ribosome during translation.

is an enzyme that winds and unwinds the DNA double helix in order to increase or decrease DNA supercoiling. By controlling supercoiling, topoisomerase indirectly controls DNA transcription, as a highly supercoiled molecule is difficult to access and transcribe while a relaxed helix is easier to access. Topoisomerase I functions by cutting one strand of DNA and then resealing it after adding or removing a helix rotation. In contrast, type II topoisomerases cut both DNA strands. Both type I and type II enzymes exists in prokaryotes and eukaryotes.

The name topoisomerase is indicative of its function, as the cut and uncut DNA helices are isomers because only their topology has been changed. Thus, the name topoisomerase.

Function

First, topoisomerase I binds to DNA and cuts one strand while simultaneously forming a covalent phosphoester bond between the 5’ end of the cut DNA strand and one of topoisomerase’s , specifically tyrosine. The free 3’ end of cut DNA is held by the enzyme noncovalently. Then the non-cleaved DNA strand is passed through the cleaved ends and, finally, the cleaved strand is reattached, unwinding the helix by one rotation.

Topoisomerase is essential to DNA transcription and replication because it decreases DNA supercoiling ahead of the replication fork. Without this enzyme, supercoiling would prevent the ability of DNA or RNA polymerases to move down a DNA strand. This process of removing supercoils is favorable and therefore does not require any added energy. However, topoisomerase does require energy to add helix rotations and increase supercoiling. This is important for compacting DNA when transcription and replication are not occuring.

Structural Highlights

Topoisomerase is a single protein chain consisting of . It can be separated into four domains. Domain I has 1 beta pleated sheet and 4 alpha helices, and is most likely responsible for binding topoisomerase to DNA. Domain II is made up of 2 beta pleated sheets and 1 alpha helix. Domain III is made up of 5 alpha helices, and it contains , which is the catalytic part of tyrosine's active site. Domain IV contains 8 alpha helices, and it is most likely responsible for providing the overall structure and support of topoisomerase.