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110370
DSB repair by protein machines
Description
Protein Form and Function Mind Map on DSB repair by protein machines, created by sophie_connor on 27/05/2013.
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protein form and function
protein form and function
Mind Map by
sophie_connor
, updated more than 1 year ago
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Created by
sophie_connor
over 11 years ago
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Resource summary
DSB repair by protein machines
Nucleases
Cutting enzymes
Cleave nucleic acids
Exonucleases
Remove terminal nucleotides from 5' and 3'
DNA replication
Polymerase is very accurate and has its own nuclease
It can go back and immediately cut out damage
3'-5' exonuclease removes mis-incorporated nucleotides
Eukaryotes
DNA pol delta and gamma
E.coli
Pol 1
DNA repair and recombination
Damage is recognised and cut out
DNA polymerase fills gap and DNA ligase secures
NHEJ
Own 3' nuclease
If nuclease is left free it will cut DNA and genetic information will be lost
Ku binds DNA to protect ends from nuclease
Endonucleases
Cleave internal bonds
RNases
DNases
Can drive reactions forwards or backwards due to their equilibrium
DNA ligase
Co factors
Ecoli
NAD+
Eukaryotes
ATP
Need 5' P and 3' OH
Makes phosphodiester bond
Ligase binds ATP
Hydrolyses ATP to AMP
Attaches AMP to itself via a lysine bond
Uses energy to facilitate bond formation
Ligase transfers phosphate moiety to other side forming ADP
Enzyme catalyses attack of OH
AMP released back into solution
Ligation assay using gel to follow molecule getting larger
Types of DNA ends
Blunt ends
Sticky ends
Incompatible ends
Non homolgous end joining
Bacteria
Ku binds ends of DNA break
Polymerase fills DNA gap bringing ends together
Phosphodiesterase cleaves nucleotides from DNA leaving 3' OH and 5'P
Ligase repairs DNA nick
If polymerases aren't controlled they will keep synthesising DNA resulting in displacement of original DNA
Nuclease removes unwanted DNA
Bacterial DNA ligases
LigD is ATP dependent DNA ligase
Multidomain protein
Polymerase, nuclease and ligase
Can add nucleotides to ssDNA or blunt dsDNA in a template independent manner
PolDom can fill in ss gaps to extend 3' resected primers
PolDom inserts nucleotides opposite 8-oxoG and extends base pair
PolDom dislocates and realigns template strand
Important for abasic sites
Microhomology mediated DSB repair
DSB with complementary overhangs only needs ligase from LigD as it can be aligned properly
When ends are not complementary Ku-LigD complex searches for areas of microhomology to form a synpatic complex
Aligns break, resection, gap filling and ligation
Eukaryotes
Ku70/80 heterodimer binds DNA ends
DNA-PKcs recruited and activated
DNA-Pkcs form complex with Artemis
Artemis is a 5'-3' exonuclease activated by DNA-PKcs
Processes broken ends and prepares them for ligation
Ligation carried out by XRCC4/Cernunnos XLF/DNA ligase IV
Formation of AMP complex called adenylate complex
AMP moiety transferred to DNA adenylate complex
LIgase catalyses attack by 3'OH to join the polynucleotides and release AMP
Prokaryotes
Ku binds to 3' end and recruits LigD which recognises 5'P
Non-extendable 3' termini can be resected by NucDom of LigD
Resynthesised by PolDom and ligation occurs
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