FENs (flap endonucleases) and related FEN-like enzymes [EXO-1 (exonuclease-1), GEN-1 (gap endonuclease 1) and XPG (xeroderma pigmentosum complementation group G)] are a family of bivalent-metal-ion-dependent nucleases that catalyse structure-specific hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair and recombination. In the case of FENs, the ability to catalyse reactions on a variety of substrates has been rationalized as a result of combined functional and structural studies. Analyses of FENs also exemplify controversies regarding the two-metal-ion mechanism. However, kinetic studies of T5FEN (bacteriophage T5 FEN) reveal that a two-metal-ion-like mechanism for chemical catalysis is plausible. Consideration of the metallobiochemistry and the positioning of substrate in metal-free structures has led to the proposal that the duplex termini of substrates are unpaired in the catalytically active form and that FENs and related enzymes may recognize breathing duplex termini within more complex structures. An outstanding issue in FEN catalysis is the role played by the intermediate (I) domain arch or clamp. It has been proposed that FENs thread the 5′-portion of their substrates through this arch, which is wide enough to accommodate single-stranded, but not double-stranded, DNA. However, FENs exhibit gap endonuclease activity acting upon substrates that have a region of 5′-duplex. Moreover, the action of other FEN family members such as GEN-1, proposed to target Holliday junctions without termini, appears incompatible with a threading mechanism. An alterative is that the I domain is used as a clamp. A future challenge is to clarify the role of this domain in FENs and related enzymes.
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April 2010
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Conference Article|
March 22 2010
Substrate recognition and catalysis by flap endonucleases and related enzymes
Christopher G. Tomlinson;
Christopher G. Tomlinson
*Centre for Chemical Biology, Department of Chemistry, Krebs Institute, University of Sheffield, Sheffield S3 7HF, U.K.
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John M. Atack;
John M. Atack
*Centre for Chemical Biology, Department of Chemistry, Krebs Institute, University of Sheffield, Sheffield S3 7HF, U.K.
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Brian Chapados;
Brian Chapados
†Skaggs Institute for Chemical Biology, The Scripps Research Institute, Department of Molecular Biology MB4, 10550 North Torrey Pines Road, La Jolla, CA 92037, U.S.A.
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John A. Tainer;
John A. Tainer
†Skaggs Institute for Chemical Biology, The Scripps Research Institute, Department of Molecular Biology MB4, 10550 North Torrey Pines Road, La Jolla, CA 92037, U.S.A.
‡Life Sciences Division, Department of Molecular Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, U.S.A.
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Jane A. Grasby
Jane A. Grasby
1
*Centre for Chemical Biology, Department of Chemistry, Krebs Institute, University of Sheffield, Sheffield S3 7HF, U.K.
1To whom correspondence should be addressed (email j.a.grasby@sheffield.ac.uk).
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Publisher: Portland Press Ltd
Received:
August 12 2009
Online ISSN: 1470-8752
Print ISSN: 0300-5127
© The Authors Journal compilation © 2010 Biochemical Society
2010
Biochem Soc Trans (2010) 38 (2): 433–437.
Article history
Received:
August 12 2009
Citation
Christopher G. Tomlinson, John M. Atack, Brian Chapados, John A. Tainer, Jane A. Grasby; Substrate recognition and catalysis by flap endonucleases and related enzymes. Biochem Soc Trans 1 April 2010; 38 (2): 433–437. doi: https://doi.org/10.1042/BST0380433
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