Resolution of Abasic Sites (AP sites)

Balakrishnan L, Brandt PD, Lindsey-Boltz LA, Sancar A, Bambara RA. Long Patch Base Excision Repair Proceeds via Coordinated Stimulation of the Multienzyme DNA Repair Complex. Journal of Biological Chemistry. 2009 May;284(22):15158–72. doi: 10.1074/jbc.m109.000505.; Guan X, Bai H, Shi G, Theriot CA, Hazra TK, Mitra S, Lu AL. The human checkpoint sensor Rad9-Rad1-Hus1 interacts with and stimulates NEIL1 glycosylase. Nucleic Acids Res. 2007;35(8):2463–72. PMID: 17395641; PMCID: PMC1885643.; Das A, Wiederhold L, Leppard JB, Kedar P, Prasad R, Wang H, Boldogh I, Karimi-Busheri F, Weinfeld M, Tomkinson AE, Wilson SH, Mitra S, Hazra TK. NEIL2-initiated, APE-independent repair of oxidized bases in DNA: Evidence for a repair complex in human cells. DNA Repair (Amst). 2006 Dec 09;5(12):1439–48. PMID: 16982218; PMCID: PMC2805168.; Smirnova E, Toueille M, Markkanen E, Hübscher U. The human checkpoint sensor and alternative DNA clamp Rad9-Rad1-Hus1 modulates the activity of DNA ligase I, a component of the long-patch base excision repair machinery. Biochem J. 2005 Jul 01;389(Pt 1):13–7. PMID: 15871698; PMCID: PMC1184534.; Wang W, Brandt P, Rossi ML, Lindsey-Boltz L, Podust V, Fanning E, Sancar A, Bambara RA. The human Rad9–Rad1–Hus1 checkpoint complex stimulates flap endonuclease 1. Proc. Natl. Acad. Sci. U.S.A. 2004 Nov 19;101(48):16762–7. doi: 10.1073/pnas.0407686101.; Wiederhold L, Leppard JB, Kedar P, Karimi-Busheri F, Rasouli-Nia A, Weinfeld M, Tomkinson AE, Izumi T, Prasad R, Wilson SH, Mitra S, Hazra TK. AP endonuclease-independent DNA base excision repair in human cells. Mol Cell. 2004 Jul 23;15(2):209–20. doi: 10.1016/j.molcel.2004.06.003. PMID: 15260972.; Dianova II, Bohr VA, Dianov GL. Interaction of human AP endonuclease 1 with flap endonuclease 1 and proliferating cell nuclear antigen involved in long-patch base excision repair. Biochemistry. 2001 Oct 23;40(42):12639–44. doi: 10.1021/bi011117i. PMID: 11601988.; Prasad R, Lavrik OI, Kim SJ, Kedar P, Yang XP, Vande Berg BJ, Wilson SH. DNA polymerase beta -mediated long patch base excision repair. Poly(ADP-ribose)polymerase-1 stimulates strand displacement DNA synthesis. J Biol Chem. 2001 Aug 31;276(35):32411–4. doi: 10.1074/jbc.c100292200. PMID: 11440997.; Masuda Y, Bennett RAO, Demple B. Dynamics of the Interaction of Human Apurinic Endonuclease (Ape1) with Its Substrate and Product. Journal of Biological Chemistry. 1998 Nov;273(46):30352–9. doi: 10.1074/jbc.273.46.30352.; Bennett RAO, Wilson DM, Wong D, Demple B. Interaction of human apurinic endonuclease and DNA polymerase ß in the base excision repair pathway. Proc. Natl. Acad. Sci. U.S.A. 1997 Jul 08;94(14):7166–9. doi: 10.1073/pnas.94.14.7166.; Klungland A, Lindahl T. Second pathway for completion of human DNA base excision-repair: reconstitution with purified proteins and requirement for DNase IV (FEN1). EMBO J. 1997 Jun 02;16(11):3341–8. PMID: 9214649; PMCID: PMC1169950.; Kubota Y, Nash RA, Klungland A, Schär P, Barnes DE, Lindahl T. Reconstitution of DNA base excision-repair with purified human proteins: interaction between DNA polymerase beta and the XRCC1 protein. The EMBO Journal. 1996 Dec;15(23):6662–70. doi: 10.1002/j.1460-2075.1996.tb01056.x.; Wilson DM, Takeshita M, Grollman AP, Demple B. Incision Activity of Human Apurinic Endonuclease (Ape) at Abasic Site Analogs in DNA. Journal of Biological Chemistry. 1995 Jul;270(27):16002–7. doi: 10.1074/jbc.270.27.16002.

Metabolites

H2O

Formula: H2O (18.0105642)

CAS ID: 7732-18-5

Nicotinamide

Formula: C6H6N2O (122.0480106)

CAS ID: 98-92-0

NAD(1-)

Formula: C21H26N7O14P2 (662.1012936000001)

CAS ID: 53-84-9



Enzyme

EC Number name full name note
3.1.-.-
3.2.2.27 uracil-DNA glycosylase uracil-DNA deoxyribohydrolase (uracil-releasing)
6.5.1.1 DNA ligase (ATP) poly(deoxyribonucleotide)-3'-hydroxyl:5'-phospho-poly(deoxyribonucleotide) ligase (ATP)


Proteins

Protein ID name full name