Crystal structure of a junction between two Z-DNA helices

Proceedings of the National Academy of Sciences of the United States of America

Volumn 107, Issue 20, 2010, Pages 9088-9092

  De Rosa, Matteo ^a,b   De Sanctis, Daniele ^c   Rosario, Ana Lucia ^b   Archer, Margarida ^b   Rich, Alexander ^d   Athanasiadis, Alekos ^a   Carrondo, Maria Armenia ^b  

^a INSTITUTO GULBENKIAN DE CIÊNCIA   (Portugal)

^b INSTITUTO DE TECNOLOGIA QUÍMICA E BIOLÓGICA   (Portugal)

^c EUROPEAN SYNCHROTRON RADIATION FACILITY   (France)

^d MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

Base stacking; DNA structure; Extruded base; X ray diffraction

Indexed keywords

ADAR1 ENZYME; CELL ENZYME; RNA; UNCLASSIFIED DRUG;

ARTICLE; BASE PAIRING; CONTROLLED STUDY; CRYSTAL STRUCTURE; DNA BINDING; DNA HELIX; ENZYME BINDING; HUMAN; INTERCALATION COMPLEX; PRIORITY JOURNAL; STOICHIOMETRY; STRUCTURE ANALYSIS;

COMPUTATIONAL BIOLOGY; CRYSTALLIZATION; DNA, Z-FORM; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; X-RAY DIFFRACTION;

EID: 77952693170     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1003182107     Document Type: Article

References (30)

1. Wang AH, et al. (1979) Molecular structure of a left-handed double helical DNA fragment at atomic resolution. Nature 282:680-686.
2. Lafer EM, Moller A, Nordheim A, Stollar BD, Rich A (1981) Antibodies specific for left-handed Z-DNA. Proc Natl Acad Sci USA 78:3546-3550.
3. Moller A, et al. (1982) Monoclonal antibodies recognize different parts of Z-DNA. J Biol Chem 257:12081-12085. (Pubitemid 13168901)
4. Arndt-Jovin DJ, et al. (1983) Left-handed Z-DNA in bands of acid-fixed polytene chromosomes. Proc Natl Acad Sci USA 80:4344-4348.
5. Nordheim A, et al. (1981) Antibodies to left-handed Z-DNA bind to interband regions of Drosophila polytene chromosomes. Nature 294:417-422. (Pubitemid 12220246)
6. Lancillotti F, Lopez MC, Arias P, Alonso C (1987) Z-DNA in transcriptionally active chromosomes. Proc Natl Acad Sci USA 84:1560-1564.
7. Lipps HJ, et al. (1983) Antibodies against Z DNA react with the macronucleus but not the micronucleus of the hypotrichous ciliate stylonychia mytilus. Cell 32:435-441.
8. Li H, et al. (2009) Human genomic Z-DNA segments probed by the Z alpha domain of ADAR1. Nucleic Acids Res 37:2737-2746.
9. Herbert A, Lowenhaupt K, Spitzner J, Rich A (1995) Chicken double-stranded RNA adenosine deaminase has apparent specificity for Z-DNA. Proc Natl Acad Sci USA 92:7550-7554.
10. Schwartz T, Behlke J, Lowenhaupt K, Heinemann U, Rich A (2001) Structure of the DLM-1-Z-DNA complex reveals a conserved family of Z-DNA-binding proteins. Nat Struct Biol 8:761-765. (Pubitemid 32803592)
11. Rothenburg S, et al. (2005) A PKR-like eukaryotic initiation factor 2alpha kinase from zebrafish contains Z-DNA binding domains instead of dsRNA binding domains. Proc Natl Acad Sci USA 102:1602-1607. (Pubitemid 40209214)
12. Kim YG, et al. (2003) A role for Z-DNA binding in vaccinia virus pathogenesis. Proc Natl Acad Sci USA 100:6974-6979. (Pubitemid 36706378)
13. Schwartz T, Rould MA, Lowenhaupt K, Herbert A, Rich A (1999) Crystal structure of the Zalpha domain of the human editing enzyme ADAR1 bound to left-handed Z-DNA. Science 284:1841-1845. (Pubitemid 29275625)
14. Kim D, Hwang HY, Kim YG, Kim KK (2009) Crystallization and preliminary x-ray crystallographic studies of the Z-DNA-binding domain of a PKR-like kinase (PKZ) in complex with Z-DNA. Acta Crystallogr F 65:267-270.
15. Ha SC, et al. (2004) A poxvirus protein forms a complex with left-handed Z-DNA: Crystal structure of a Yatapoxvirus Zalpha bound to DNA. Proc Natl Acad Sci USA 101:14367-14372.
16. Ha SC, et al. (2008) The crystal structure of the second Z-DNA binding domain of human DAI (ZBP1) in complex with Z-DNA reveals an unusual binding mode to Z-DNA. Proc Natl Acad Sci USA 105:20671-20676.
17. Placido D, Brown BA, 2nd, Lowenhaupt K, Rich A, Athanasiadis A (2007) A left-handed RNA double helix bound by the Z alpha domain of the RNA-editing enzyme ADAR1. Structure 15:395-404. (Pubitemid 46551728)
18. Athanasiadis A, et al. (2005) The crystal structure of the Zbeta domain of the RNA-editing enzyme ADAR1 reveals distinct conserved surfaces among Z-domains. J Mol Biol 351:496-507. (Pubitemid 41021936)
19. Wang G, Christensen LA, Vasquez KM (2006) Z-DNA-forming sequences generate large-scale deletions in mammalian cells. Proc Natl Acad Sci USA 103:2677-2682. (Pubitemid 43306608)
20. Ha SC, Lowenhaupt K, Rich A, Kim YG, Kim KK (2005) Crystal structure of a junction between B-DNA and Z-DNA reveals two extruded bases. Nature 437:1183-1186. (Pubitemid 41509358)
21. Johnston BH, Quigley GJ, Ellison MJ, Rich A (1991) The Z-Z junction: The boundary between two out-of-phase Z-DNA regions. Biochemistry 30:5257-5263.
22. Athanasiadis A, Rich A, Maas S (2004) Widespread A-to-I RNA editing of Alu-containing mRNAs in the human transcriptome. PLoS Biol 2:e391. (Pubitemid 40284134)
23. Yang XL, Wang AH (1997) Structural analysis of Z-Z DNA junctions with A:A and T:T mismatched base pairs by NMR. Biochemistry 36:4258-4267.
24. Kim D, et al. (2009) Base extrusion is found at helical junctions between right- and left-handed forms of DNA and RNA. Nucleic Acids Res, 13 pp:4353-4359.
25. Leslie AGW (1992) Recent changes to the MOSFLM package for processing film and image plate data. Joint CCP4 + ESF-EAMCB Newsletter on Protein Crystallography No 26 (Daresbury Laboratory, Warrington).
26. CCP4 (1994) The CCP4 suite: Programs for protein crystallography. Acta Crystallogr D 50:760-763.
27. McCoy AJ, et al. (2007) Phaser crystallographic software. J Appl Crystallogr 40:658-674.
28. Adams PD, et al. (2002) PHENIX: Building new software for automated crystallographic structure determination. Acta Crystallogr D 58:1948-1954.
29. Emsley PC, Cowtan Kevin (2004) Coot: Model-building tools for molecular graphics. Acta Crystallogr D 60:2126-2132.
30. Lu XJ, Olson WK (2003) 3DNA: A software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures. Nucleic Acids Res 31:5108-5121.