This is a default text for your page Scott H. Vanson/Sandbox 1. Click above on edit this page to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia [1] or to the article describing Jmol [2] to the rescue.
General Description
Human polymerase θ (pol θ) is large, 290kD enzyme consisting of three distinct domains [3][4]. An N-terminal helicase-like domain, whose exact cellular functions are a topic of on-going debate and research[5][6], is linked to a C-terminal, family A DNA polymerase domain by a large and disordered central region[4]. Notably, pol θ is the only known human polymerase to contain a polymerase and helicase domain in one molecule[7]. Crystal structures have been solved for the apo form of the helicase-like domain and the ternary complex of the polymerase domain. The focus of this wiki is the polymerase domain.
Pol θ is thought to promote overall genomic stability by performing several distinct cellular functions. The primary role of the enzyme is to repair of double-stranded DNA breaks as the key enzyme in an error-prone non-homologous end-joining pathway called alternative end-joining[8] or theta-mediated end-joining. Other functions include translesion synthesis, the ability of the polymerase to bypass and extend past a site of oxidative DNA damage[9], base excision repair [10], and possibly DNA replication timing [11]. Pol θ has the specialized ability to extend DNA from minimally-paired primers (termed microhomologous)Template:Cn. Repair by this enzyme is considered to error-prone due to its tendency to add or delete short indels [8].
Several types of cancer, such as breast, ovarian, and oral carcinomas, have shown significantly higher expression levels of pol θ and correlate to poorer patient outcomes[12][13][14]. Genomic studies have shown that more than half of epithelial ovarian cancers have defects in the error-free repair pathway of homologous recombination[15] and, as a result, have an increased dependence on theta-mediated end-joining [12]. Double-stranded break repair by pol θ may be thought of as a "backup" pathway which cells depend on more when the machinery involved in homologous recombination is compromised or otherwise unavailable. This enzyme has been identified as a potential therapeutic target due to overexpression in cancers in combination with studies that have shown inhibition of pol θ to sensitize human and mouse cells to radiation and chemical agents which induce double-stranded breaks[12][16][17].
Structural Highlights
Two crystal structures of the polymerase domain have been solved bound, inserting ddATP opposite tetrahydrofuran (THF, representing an abasic site) and inserting ddGTP opposite dCMP[7]. An overall assessment of the structures display the canonical . The DNA is thought to "sit" on the palm and is enclosed by the thumb and fingers.
ddATP Opposite THF
An inspection of the active site reveals the , in this instance calcium. This structure required the use of calcium, as opposed to the physiological magnesium, as the primer strand retains the 3' hydroxyl which would otherwise be subjected to nucleophilic attack. The similarly conserved lysine and arginine of the O-helix make stabilizing ionic contacts with non-bridging oxygens of the triphosphate tail of the incoming nucleotide.
dCMP Opposite ddGTP
from the same study was solved with magnesium as the coordinated metal, a 27 amino acid N-terminal truncation, and a blunted DNA oligomer to remove the 3' template overhang. The overall structure is virtually identical to the aforementioned structure complexed with calcium, with the exception of a slight shift in position of the O-helix to be closer to the cognate C:G basepair.
Structural Insights into Function
Related Proteins
This is a sample scene created with SAT to by Group, and another to make of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.
