Crystal structure of the Zα domain of the human editing enzyme ADAR1 bound to left-handed Z-DNA

Science

Volumn 284, Issue 5421, 1999, Pages 1841-1845

  Schwartz, Thomas ^a   Rould, Mark A ^b   Lowenhaupt, Ky ^a   Herbert, Alan ^a   Rich, Alexander ^a  

^a MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^b UNIVERSITY OF VERMONT   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE DEAMINASE; DNA Z; DNA; DSRNA ADENOSINE DEAMINASE; HELIX LOOP HELIX PROTEIN; WATER; GUANINE; RNA;

ARTICLE; CRYSTAL STRUCTURE; ENZYME ACTIVE SITE; ENZYME BINDING; ENZYME CONFORMATION; ENZYME SPECIFICITY; MOLECULAR DYNAMICS; MOLECULAR MODEL; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN DNA BINDING; PROTEIN SECONDARY STRUCTURE; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; STRUCTURE ANALYSIS; AMINO ACID SEQUENCE; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; HUMAN; HYDROGEN BOND; METABOLISM; MOLECULAR GENETICS; NON-PROGRAMMATIC; PROTEIN CONFORMATION; X RAY CRYSTALLOGRAPHY; CIRCULAR DICHROISM; GENETIC CODE; MOLECULAR RECOGNITION;

NON-PROGRAMMATIC;

ADENOSINE DEAMINASE; AMINO ACID SEQUENCE; BINDING SITES; CRYSTALLOGRAPHY, X-RAY; DNA; HELIX-TURN-HELIX MOTIFS; HUMANS; HYDROGEN BONDING; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY; SUBSTRATE SPECIFICITY; WATER;

EID: 0033546005     PISSN: 00368075     EISSN: None     Source Type: Journal    
DOI: 10.1126/science.284.5421.1841     Document Type: Article

References (46)

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9. The protein construct used here was originally named Za (7). It is structurally homogeneous, unlike other published Zα peptides. For simplicity, here we use the generic name Zα instead of Za.
10. 170.
11. 170.
12. 2- and COOH-termini of the protein are disordered. The structure is defined for residues 134 to 198 of the Zα monomer in complex I, 136 to 199 in complex II, and 134 to 199 in complex III. The DNA structure is well resolved except for the 5′-dT overhang, which appears to be disordered.
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15. Single-letter abbreviations for amino acid residues are as follows: A, Ala; C, Cys; D, Asp; E, Glu; F, Phe; G, Gly; H, His; I, Ile; K, Lys; L, Leu; M, Met; N, Asn; P, Pro; Q, Gln; R, Arg; S, Ser; T. Thr; V, Val; W, Trp; and Y, Tyr.
16. Rmsd is 0.93 Å between complex I and II, 1.07 Å between complex II and III, and 0.76 Å between complex I and III, including all protein and DNA atoms, even though the three complexes were built and refined entirely independently.
17. α atoms 1.28 Å).
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20. Structures: HNF-3γ [K. L. Clark, E. D. Halay, E. Lai, S. K. Burley, Nature 364, 412 (1993)], SmtB [ W. J. Cook, S. R. Kar, K. B. Taylor, L. M. Hall, J. Mol. Biol. 275, 337 (1998)] , CAP [S. C Schultz, G. C. Shields, T. A. Steitz, Science 253, 1001 (1991)], H5 [ V. Ramakrishnan, J. T. Finch, V. Graziano, P. L. Lee, R. M. Sweet, Nature 362, 219 (1993)], OCT-1 [J. D. Klemm, M. A. Rould, R. Aurora, W. Herr, C. O. Pabo, Cell 77, 21 (1994)], and PAX-6 [ H. E. Xu et al., Genes Dev., in press].
21. Structures: HNF-3γ [K. L. Clark, E. D. Halay, E. Lai, S. K. Burley, Nature 364, 412 (1993)], SmtB [ W. J. Cook, S. R. Kar, K. B. Taylor, L. M. Hall, J. Mol. Biol. 275, 337 (1998)] , CAP [S. C Schultz, G. C. Shields, T. A. Steitz, Science 253, 1001 (1991)], H5 [ V. Ramakrishnan, J. T. Finch, V. Graziano, P. L. Lee, R. M. Sweet, Nature 362, 219 (1993)], OCT-1 [J. D. Klemm, M. A. Rould, R. Aurora, W. Herr, C. O. Pabo, Cell 77, 21 (1994)], and PAX-6 [ H. E. Xu et al., Genes Dev., in press].
22. Structures: HNF-3γ [K. L. Clark, E. D. Halay, E. Lai, S. K. Burley, Nature 364, 412 (1993)], SmtB [ W. J. Cook, S. R. Kar, K. B. Taylor, L. M. Hall, J. Mol. Biol. 275, 337 (1998)] , CAP [S. C Schultz, G. C. Shields, T. A. Steitz, Science 253, 1001 (1991)], H5 [ V. Ramakrishnan, J. T. Finch, V. Graziano, P. L. Lee, R. M. Sweet, Nature 362, 219 (1993)], OCT-1 [J. D. Klemm, M. A. Rould, R. Aurora, W. Herr, C. O. Pabo, Cell 77, 21 (1994)], and PAX-6 [ H. E. Xu et al., Genes Dev., in press].
23. Structures: HNF-3γ [K. L. Clark, E. D. Halay, E. Lai, S. K. Burley, Nature 364, 412 (1993)], SmtB [ W. J. Cook, S. R. Kar, K. B. Taylor, L. M. Hall, J. Mol. Biol. 275, 337 (1998)] , CAP [S. C Schultz, G. C. Shields, T. A. Steitz, Science 253, 1001 (1991)], H5 [ V. Ramakrishnan, J. T. Finch, V. Graziano, P. L. Lee, R. M. Sweet, Nature 362, 219 (1993)], OCT-1 [J. D. Klemm, M. A. Rould, R. Aurora, W. Herr, C. O. Pabo, Cell 77, 21 (1994)], and PAX-6 [ H. E. Xu et al., Genes Dev., in press].
24. Structures: HNF-3γ [K. L. Clark, E. D. Halay, E. Lai, S. K. Burley, Nature 364, 412 (1993)], SmtB [ W. J. Cook, S. R. Kar, K. B. Taylor, L. M. Hall, J. Mol. Biol. 275, 337 (1998)] , CAP [S. C Schultz, G. C. Shields, T. A. Steitz, Science 253, 1001 (1991)], H5 [ V. Ramakrishnan, J. T. Finch, V. Graziano, P. L. Lee, R. M. Sweet, Nature 362, 219 (1993)], OCT-1 [J. D. Klemm, M. A. Rould, R. Aurora, W. Herr, C. O. Pabo, Cell 77, 21 (1994)], and PAX-6 [ H. E. Xu et al., Genes Dev., in press].
25. S. C. Harrison and A. K. Aggarwal, Annu. Rev. Bioehem. 59, 933 (1990); C. O. Pabo and R. T. Sauer, ibid. 61, 1053 (1992).
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30. Program tools: X-PLOR [A. T. Brünger, X-PLOK Version 3.1. A System for X-ray Crystallography and NMR (Yale Univ. Press, New Haven, CT, 1992)], HKL package [Z. Otwinowski and W. Minor, Methods Enzymol. 276A, 307 (1997)], SOLVE [T. C. Terwilliger and J. Berendzen, Acta Crystallogr. D52, 749 (1996)], DM [K. Cowtan and P. Main, ibid., p. 43 (1996)] , and Procheck [A. L. Morris, M. W. MacArthur, E. G. Hutchinson, J. M. Thornton, Proteins 12, 345 (1992)].
31. Program tools: X-PLOR [A. T. Brünger, X-PLOK Version 3.1. A System for X-ray Crystallography and NMR (Yale Univ. Press, New Haven, CT, 1992)], HKL package [Z. Otwinowski and W. Minor, Methods Enzymol. 276A, 307 (1997)], SOLVE [T. C. Terwilliger and J. Berendzen, Acta Crystallogr. D52, 749 (1996)], DM [K. Cowtan and P. Main, ibid., p. 43 (1996)] , and Procheck [A. L. Morris, M. W. MacArthur, E. G. Hutchinson, J. M. Thornton, Proteins 12, 345 (1992)].
32. Program tools: X-PLOR [A. T. Brünger, X-PLOK Version 3.1. A System for X-ray Crystallography and NMR (Yale Univ. Press, New Haven, CT, 1992)], HKL package [Z. Otwinowski and W. Minor, Methods Enzymol. 276A, 307 (1997)], SOLVE [T. C. Terwilliger and J. Berendzen, Acta Crystallogr. D52, 749 (1996)], DM [K. Cowtan and P. Main, ibid., p. 43 (1996)] , and Procheck [A. L. Morris, M. W. MacArthur, E. G. Hutchinson, J. M. Thornton, Proteins 12, 345 (1992)].
33. Program tools: X-PLOR [A. T. Brünger, X-PLOK Version 3.1. A System for X-ray Crystallography and NMR (Yale Univ. Press, New Haven, CT, 1992)], HKL package [Z. Otwinowski and W. Minor, Methods Enzymol. 276A, 307 (1997)], SOLVE [T. C. Terwilliger and J. Berendzen, Acta Crystallogr. D52, 749 (1996)], DM [K. Cowtan and P. Main, ibid., p. 43 (1996)] , and Procheck [A. L. Morris, M. W. MacArthur, E. G. Hutchinson, J. M. Thornton, Proteins 12, 345 (1992)].
34. 2 of protein surface area is lost upon binding [E. Fraenkel, M. A. Rould, K. A. Chambers, C. O. Pabo, J. Mol. Biol. 284, 351 (1998)].
35. 2 is 30 nM, as determined by ultracentrifugation (M. Schade et al., unpublished data).
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37. L. F. Liu and J. C. Wang, Proc. Natl. Acad. Sci. U.S.A. 84, 7024 (1987); B. Wittig, T. Dorbic, A. Rich, ibid. 88, 2259 (1991); B. Wittig, S. Wölfl, T. Dorbic, W. Vahrson, A. Rich, EMBO J. 11, 4653 (1992).
38. L. F. Liu and J. C. Wang, Proc. Natl. Acad. Sci. U.S.A. 84, 7024 (1987); B. Wittig, T. Dorbic, A. Rich, ibid. 88, 2259 (1991); B. Wittig, S. Wölfl, T. Dorbic, W. Vahrson, A. Rich, EMBO J. 11, 4653 (1992).
39. S. Maas, T. Melcher, P. H. Seeburg, Curr. Opin. Cell Biol. 9, 343 (1997).
40. A. Herbert and A. Rich, J. Biol. Chem. 271, 11595 (1996).
41. T. Schwartz et al., Acta Crystallogr., in press.
42. Figures were made with MOLSCRIPT (Figs. 1 and 2A) [P. J. Kraulis, J. Appl. Crstallogr. 24, 946 (1991)], Bobscript(Fig. 3A) [R. M. Esnouf, J. Mol. Graphics 15, 132 (1997)], and RASTER-3D [ E. A. Merritt and E. P. Murphy, Acta Crystallogr. D 50, 869 (1994)]. Figure 3B was made with GRASP [A. Nicholls, K. A. Sharp, B. Honig, Proteins Struct. Funct. Genet. 11, 281 (1991)].
43. Figures were made with MOLSCRIPT (Figs. 1 and 2A) [P. J. Kraulis, J. Appl. Crstallogr. 24, 946 (1991)], Bobscript(Fig. 3A) [R. M. Esnouf, J. Mol. Graphics 15, 132 (1997)], and RASTER-3D [ E. A. Merritt and E. P. Murphy, Acta Crystallogr. D 50, 869 (1994)]. Figure 3B was made with GRASP [A. Nicholls, K. A. Sharp, B. Honig, Proteins Struct. Funct. Genet. 11, 281 (1991)].
44. Figures were made with MOLSCRIPT (Figs. 1 and 2A) [P. J. Kraulis, J. Appl. Crstallogr. 24, 946 (1991)], Bobscript(Fig. 3A) [R. M. Esnouf, J. Mol. Graphics 15, 132 (1997)], and RASTER-3D [ E. A. Merritt and E. P. Murphy, Acta Crystallogr. D 50, 869 (1994)]. Figure 3B was made with GRASP [A. Nicholls, K. A. Sharp, B. Honig, Proteins Struct. Funct. Genet. 11, 281 (1991)].
45. Figures were made with MOLSCRIPT (Figs. 1 and 2A) [P. J. Kraulis, J. Appl. Crstallogr. 24, 946 (1991)], Bobscript(Fig. 3A) [R. M. Esnouf, J. Mol. Graphics 15, 132 (1997)], and RASTER-3D [ E. A. Merritt and E. P. Murphy, Acta Crystallogr. D 50, 869 (1994)]. Figure 3B was made with GRASP [A. Nicholls, K. A. Sharp, B. Honig, Proteins Struct. Funct. Genet. 11, 281 (1991)].
46. Supported by grants from the National Institutes of Health and the National Science Foundation and by a fellowship from the German Academic Exchange Service (DAAD) to T.S. Coordinates for the crystal structure have been deposited in the Protein Data Bank (accession code 1QBJ).