Processing of DNA double-strand break ends

Parameswaran B, Chiang H, Lu Y, Coates J, Deng C, Baer R, Lin H, Li R, Paull TT, Hu Y. Damage-induced BRCA1 phosphorylation by Chk2 contributes to the timing of end resection. Cell Cycle. 2015 Feb 01;14(3):437–48. doi: 10.4161/15384101.2014.972901.; Davies OR, Forment JV, Sun M, Belotserkovskaya R, Coates J, Galanty Y, Demir M, Morton CR, Rzechorzek NJ, Jackson SP, Pellegrini L. CtIP tetramer assembly is required for DNA-end resection and repair. Nature Structural & Molecular Biology. 2015 Jan 05;22(2):150–7. doi: 10.1038/nsmb.2937.; Sturzenegger A, Burdova K, Kanagaraj R, Levikova M, Pinto C, Cejka P, Janscak P. DNA2 Cooperates with the WRN and BLM RecQ Helicases to Mediate Long-range DNA End Resection in Human Cells. Journal of Biological Chemistry. 2014 Sep;289(39):27314–26. doi: 10.1074/jbc.m114.578823.; Wang H, Shi LZ, Wong CCL, Han X, Hwang PY, Truong LN, Zhu Q, Shao Z, Chen DJ, Berns MW, Yates JR, Chen L, Wu X. The Interaction of CtIP and Nbs1 Connects CDK and ATM to Regulate HR–Mediated Double-Strand Break Repair. PLoS Genet. 2013 Feb 28;9(2):e1003277. doi: 10.1371/journal.pgen.1003277.; Buis J, Stoneham T, Spehalski E, Ferguson DO. Mre11 regulates CtIP-dependent double-strand break repair by interaction with CDK2. Nature Structural & Molecular Biology. 2012 Jan 08;19(2):246–52. doi: 10.1038/nsmb.2212.; Cotta-Ramusino C, McDonald ER, Hurov K, Sowa ME, Harper JW, Elledge SJ. A DNA damage response screen identifies RHINO, a 9-1-1 and TopBP1 interacting protein required for ATR signaling. Science. 2011 Jun 10;332(6035):1313–7. PMID: 21659603; PMCID: PMC4357496.; Nimonkar AV, Genschel J, Kinoshita E, Polaczek P, Campbell JL, Wyman C, Modrich P, Kowalczykowski SC. BLM-DNA2-RPA-MRN and EXO1-BLM-RPA-MRN constitute two DNA end resection machineries for human DNA break repair. Genes Dev. 2011 Feb 15;25(4):350–62. PMID: 21325134; PMCID: PMC3042158.; Suhasini AN, Rawtani NA, Wu Y, Sommers JA, Sharma S, Mosedale G, North PS, Cantor SB, Hickson ID, Brosh RM. Interaction between the helicases genetically linked to Fanconi anemia group J and Bloom's syndrome. EMBO J. 2011 Feb 16;30(4):692–705. PMID: 21240188; PMCID: PMC3041957.; Ciccia A, Elledge SJ. The DNA Damage Response: Making It Safe to Play with Knives. Molecular Cell. 2010 Oct;40(2):179–204. doi: 10.1016/j.molcel.2010.09.019.; Yun MH, Hiom K. CtIP-BRCA1 modulates the choice of DNA double-strand-break repair pathway throughout the cell cycle. Nature. 2009 May 21;459(7245):460–3. PMID: 19357644; PMCID: PMC2857324.; Chen L, Nievera CJ, Lee AY, Wu X. Cell Cycle-dependent Complex Formation of BRCA1·CtIP·MRN Is Important for DNA Double-strand Break Repair. Journal of Biological Chemistry. 2008 Mar;283(12):7713–20. doi: 10.1074/jbc.m710245200.

Metabolites

H2O

Formula: H2O (18.0105642)

CAS ID: 7732-18-5

Nicotinamide

Formula: C6H6N2O (122.0480106)

CAS ID: 98-92-0

Zinc cation

Formula: Zn (63.929145)

CAS ID: 23713-49-7

ATP(4-)

Formula: C10H12N5O13P3 (502.9644492)

CAS ID:

NAD(1-)

Formula: C21H26N7O14P2 (662.1012936000001)

CAS ID: 53-84-9

ADP(3-)

Formula: C10H12N5O10P2 (424.0059412)

CAS ID:



Enzyme

EC Number name full name note
2.3.1.-
2.1.1.357 [histone H3]-lysine36 N-dimethyltransferase S-adenosyl-L-methionine:[histone H3]-L-lysine36 N6-dimethyltransferase
2.3.1.286 protein acetyllysine N-acetyltransferase [protein]-N6-acetyl-L-lysine:NAD+ N-acetyltransferase (NAD+-hydrolysing; 2''-O-acetyl-ADP-D-ribose-forming)
2.3.1.48 histone acetyltransferase acetyl-CoA:[protein]-L-lysine acetyltransferase
2.3.2.23 E2 ubiquitin-conjugating enzyme S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine:[E2 ubiquitin-conjugating enzyme] ubiquitinyl transferase
2.3.2.26 HECT-type E3 ubiquitin transferase [E2 ubiquitin-conjugating enzyme]-S-ubiquitinyl-L-cysteine:[acceptor protein] ubiquitin transferase (isopeptide bond-forming)
2.3.2.27 RING-type E3 ubiquitin transferase [E2 ubiquitin-conjugating enzyme]-S-ubiquitinyl-L-cysteine:[acceptor protein] ubiquitin transferase (isopeptide bond-forming; RING-type)
2.7.11.1 non-specific serine/threonine protein kinase ATP:protein phosphotransferase (non-specific)
2.7.11.22 cyclin-dependent kinase ATP:cyclin phosphotransferase
3.1.3.16 protein-serine/threonine phosphatase protein-serine/threonine-phosphate phosphohydrolase
3.6.4.12 DNA helicase
5.6.2.3 DNA 5'-3' helicase DNA 5'-3' helicase (ATP-hydrolysing)
5.6.2.4 DNA 3'-5' helicase DNA 3'-5' helicase (ATP-hydrolysing)


Proteins

Protein ID name full name