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LigA is a relevant example as it is structurally similar to a clade of enzymes found across all types of bacteria. [7] Ligases have a metal binding site which is capable of recognizing nicks in DNA. The ligase forms a DNA-adenylate complex, assisting recognition. [8] With human DNA ligase, this forms a crystallized complex.
DNA gyrase, or simply gyrase, is an enzyme within the class of topoisomerase and is a subclass of Type II topoisomerases [1] that reduces topological strain in an ATP dependent manner while double-stranded DNA is being unwound by elongating RNA-polymerase [2] or by helicase in front of the progressing replication fork.
Type II topoisomerases increase or decrease the linking number of a DNA loop by 2 units, and it promotes chromosome disentanglement. For example, DNA gyrase, a type II topoisomerase observed in E. coli and most other prokaryotes, introduces negative supercoils and decreases the linking number by 2.
A hindrance in the free rotation of DNA might arise due to a topological constraint, causing the DNA in front of RNAP to become over-twisted (positively supercoiled) and the DNA behind RNAP would become under-twisted (negatively supercoiled). It has been found that a topological constraint is not needed because RNAP generates sufficient torque ...
Integration host factor, IHF, is not a nucleoid-associated protein only found in gram negative bacteria. [15] It is a 20 kDa heterodimer, composed of α and β subunits that bind to the sequence 5' - WATCAANNNNTTR - 3' and bends the DNA approximately 160 degrees. [16] The β arms of IHF have Proline residues that help stabilize the DNA kinks.
Negative supercoils favor local unwinding of the DNA, allowing processes such as transcription, DNA replication, and recombination. Negative supercoiling is also thought to favour the transition between B-DNA and Z-DNA , and moderate the interactions of DNA binding proteins involved in gene regulation .
Where DNA gyrase forms a tetramer and is capable of cleaving a double-stranded region of DNA, reverse gyrase can only cleave single stranded DNA. [ 3 ] [ 4 ] More specifically, reverse gyrase is a member of the type IA topoisomerase class; along with the ability to relax negatively or positively supercoiled DNA [ 5 ] (which does not require ATP ...
A-DNA is a form of DNA that occurs when the DNA is in a dehydrated state or is bound to certain proteins, and it has a shorter and wider helix than B-DNA. The helix of A-DNA is also tilted and compressed compared to B-DNA. A-DNA is believed to play a role in certain biological processes, such as DNA replication and gene expression.