Coordination of Steps in Single-nucleotide Base Excision Repair Mediated by Apurinic/Apyrimidinic Endonuclease 1 and DNA Polymerase β

• Published in: The Journal of biological chemistry 2007-05, Vol.282 (18), p.13532-13541
• Main Authors: Liu, Yuan, Prasad, Rajendra, Beard, William A., Kedar, Padmini S., Hou, Esther W., Shock, David D., Wilson, Samuel H.
• Format: Article
• Language: English
• Subjects: DNA - chemistry; DNA - metabolism; DNA Polymerase beta - chemistry; DNA Polymerase beta - metabolism; DNA Repair - physiology; DNA-(Apurinic or Apyrimidinic Site) Lyase - chemistry; DNA-(Apurinic or Apyrimidinic Site) Lyase - metabolism; Humans; Multiprotein Complexes - chemistry; Multiprotein Complexes - metabolism; Phosphates - chemistry; Phosphates - metabolism; Protein Binding - physiology; Protein Structure, Quaternary; Substrate Specificity
• ISSN: 0021-9258; 1083-351X
• DOI: 10.1074/jbc.M611295200

The individual steps in single-nucleotide base excision repair (SN-BER) are coordinated to enable efficient repair without accumulation of cytotoxic DNA intermediates. The DNA transactions and various proteins involved in SN-BER of abasic sites are well known in mammalian systems. Yet, despite a wealth of information on SN-BER, the mechanism of step-by-step coordination is poorly understood. In this study we conducted experiments toward understanding step-by-step coordination during BER by comparing DNA binding specificities of two major human SN-BER enzymes, apurinic/aprymidinic endonuclease 1 (APE) and DNA polymerase β (Pol β). It is known that these enzymes do not form a stable complex in solution. For each enzyme, we found that DNA binding specificity appeared sufficient to explain the sequential processing of BER intermediates. In addition, however, we identified at higher enzyme concentrations a ternary complex of APE·Pol β·DNA that formed specifically at BER intermediates containing a 5′-deoxyribose phosphate group. Formation of this ternary complex was associated with slightly stronger Pol β gap-filling and much stronger 5′-deoxyribose phosphate lyase activities than was observed with the Pol β·DNA binary complex. These results indicate that step-by-step coordination in SN-BER can rely on DNA binding specificity inherent in APE and Pol β, although coordination also may be facilitated by APE·Pol β·DNA ternary complex formation with appropriate enzyme expression levels or enzyme recruitment to sites of repair.