Novel DNA binding motifs in the DNA repair enzyme endonuclease III crystal structure - PubMed (original) (raw)
Novel DNA binding motifs in the DNA repair enzyme endonuclease III crystal structure
M M Thayer et al. EMBO J. 1995.
Abstract
The 1.85 A crystal structure of endonuclease III, combined with mutational analysis, suggests the structural basis for the DNA binding and catalytic activity of the enzyme. Helix-hairpin-helix (HhH) and [4Fe-4S] cluster loop (FCL) motifs, which we have named for their secondary structure, bracket the cleft separating the two alpha-helical domains of the enzyme. These two novel DNA binding motifs and the solvent-filled pocket in the cleft between them all lie within a positively charged and sequence-conserved surface region. Lys120 and Asp138, both shown by mutagenesis to be catalytically important, lie at the mouth of this pocket, suggesting that this pocket is part of the active site. The positions of the HhH motif and protruding FCL motif, which contains the DNA binding residue Lys191, can accommodate B-form DNA, with a flipped-out base bound within the active site pocket. The identification of HhH and FCL sequence patterns in other DNA binding proteins suggests that these motifs may be a recurrent structural theme for DNA binding proteins.
Similar articles
- Atomic structure of the DNA repair [4Fe-4S] enzyme endonuclease III.
Kuo CF, McRee DE, Fisher CL, O'Handley SF, Cunningham RP, Tainer JA. Kuo CF, et al. Science. 1992 Oct 16;258(5081):434-40. doi: 10.1126/science.1411536. Science. 1992. PMID: 1411536 - Crystal structures of human DNA polymerase beta complexed with DNA: implications for catalytic mechanism, processivity, and fidelity.
Pelletier H, Sawaya MR, Wolfle W, Wilson SH, Kraut J. Pelletier H, et al. Biochemistry. 1996 Oct 1;35(39):12742-61. doi: 10.1021/bi952955d. Biochemistry. 1996. PMID: 8841118 - Identification of the Archaeoglobus fulgidus endonuclease III DNA interaction surface using heteronuclear NMR methods.
Shekhtman A, McNaughton L, Cunningham RP, Baxter SM. Shekhtman A, et al. Structure. 1999 Aug 15;7(8):919-30. doi: 10.1016/s0969-2126(99)80119-1. Structure. 1999. PMID: 10467137 - Three-dimensional structural views of damaged-DNA recognition: T4 endonuclease V, E. coli Vsr protein, and human nucleotide excision repair factor XPA.
Morikawa K, Shirakawa M. Morikawa K, et al. Mutat Res. 2000 Aug 30;460(3-4):257-75. doi: 10.1016/s0921-8777(00)00031-8. Mutat Res. 2000. PMID: 10946233 Review. - [Crystal structure and function of pyrimidine dimer specific excision repair enzyme: T4 endonuclease V].
Ariyoshi M, Morikawa K. Ariyoshi M, et al. Nihon Rinsho. 1993 Nov;51(11):3031-41. Nihon Rinsho. 1993. PMID: 8277587 Review. Japanese.
Cited by
- Disentangling Unusual Catalytic Properties and the Role of the [4Fe-4S] Cluster of Three Endonuclease III from the Extremophile D. radiodurans.
Rollo F, Borges PT, Silveira CM, Rosa MTG, Todorovic S, Moe E. Rollo F, et al. Molecules. 2022 Jul 2;27(13):4270. doi: 10.3390/molecules27134270. Molecules. 2022. PMID: 35807515 Free PMC article. - Biochemical and functional characterization of an endonuclease III from Thermococcus barophilus Ch5.
Tang C, Jiang D, Zhang L. Tang C, et al. World J Microbiol Biotechnol. 2022 Jun 25;38(8):145. doi: 10.1007/s11274-022-03328-y. World J Microbiol Biotechnol. 2022. PMID: 35750964 - Function and Molecular Mechanism of the DNA Damage Response in Immunity and Cancer Immunotherapy.
Ye Z, Shi Y, Lees-Miller SP, Tainer JA. Ye Z, et al. Front Immunol. 2021 Dec 14;12:797880. doi: 10.3389/fimmu.2021.797880. eCollection 2021. Front Immunol. 2021. PMID: 34970273 Free PMC article. Review. - Decoding Cancer Variants of Unknown Significance for Helicase-Nuclease-RPA Complexes Orchestrating DNA Repair During Transcription and Replication.
Tsutakawa SE, Bacolla A, Katsonis P, Bralić A, Hamdan SM, Lichtarge O, Tainer JA, Tsai CL. Tsutakawa SE, et al. Front Mol Biosci. 2021 Dec 14;8:791792. doi: 10.3389/fmolb.2021.791792. eCollection 2021. Front Mol Biosci. 2021. PMID: 34966786 Free PMC article. - Caught in motion: human NTHL1 undergoes interdomain rearrangement necessary for catalysis.
Carroll BL, Zahn KE, Hanley JP, Wallace SS, Dragon JA, Doublié S. Carroll BL, et al. Nucleic Acids Res. 2021 Dec 16;49(22):13165-13178. doi: 10.1093/nar/gkab1162. Nucleic Acids Res. 2021. PMID: 34871433 Free PMC article.
References
- Mol Cell Biol. 1987 Jan;7(1):26-32 - PubMed
- Proc Natl Acad Sci U S A. 1992 Sep 15;89(18):8779-83 - PubMed
- Proc Natl Acad Sci U S A. 1985 Jan;82(2):474-8 - PubMed
- Proc Natl Acad Sci U S A. 1989 Jun;86(12):4412-5 - PubMed
- Proc Natl Acad Sci U S A. 1988 Apr;85(8):2444-8 - PubMed
Publication types
MeSH terms
Substances
LinkOut - more resources
Full Text Sources
Other Literature Sources
Molecular Biology Databases
Research Materials