DNA Polymerase I: Difference between revisions

==Structure of the Klenow fragment==

Thomas Steitz determined the X-ray structure of Klenow fragment in complex with a 13-nucleotide (nt) primer strand and a 10-nt template strand<ref>PMID: 8469987</ref> (1kln; the primer strand is the strand that is synthesized by the polymerase as the complement of the template strand; the entire DNA is often referred to as primer−template DNA). <scene name='Sandbox_dvoet/DNA_polymerase/Klenow-dna/4'>Here</scene> Klenow fragment is shown in ribbon form colored in rainbow order from its N-terminus (''blue'') to its C-terminus (''red''). The DNA is drawn in stick form and colored according to atom type with template C cyan, primer C magenta, N blue, O red, and P orange and with an orange rod connecting successive P atoms in each strand. The 3' → 5' exonuclease active site at the  N-terminal end of the protein is marked by a Zn²⁺ ion (''gray sphere''). 'The arrangement of the polymerase's three  domains is reminiscent of a right hand grasping a rod (the DNA) and hence, from N- to C-terminus, they are named “palm“, "fingers", and "thumb". The polymerase's active site is located in the palm domain near the cleft between the fingers and thumb domains. All DNA polymerases of known structure have a similar spatial arrangements  of fingers, thumb, and palm domains, even though, in many cases, they have no recognizable sequence similarity with Pol I and the structure of their fingers, thumb, and palm domains bear no resemblance to those of Pol I.