Crystallographic snapshots along a protein-induced DNA-bending pathway.

Two new high-resolution cocrystal structures of EcoRV endonuclease bound to DNA show that a large variation in DNA-bending angles is sampled in the ground state binary complex. Together with previous structures, these data reveal a contiguous series of protein conformational states delineating a specific trajectory for the induced-fit pathway. Rotation of the DNA-binding domains, together with movements of two symmetry-related helices binding in the minor groove, causes base unstacking at a key base-pair step and propagates structural changes that assemble the active sites. These structures suggest a complex mechanism for DNA bending that depends on forces generated by interacting protein segments, and on selective neutralization of phosphate charges along the inner face of the bent double helix.

[1]  M. A. Fabian,et al.  Electrostatic mechanism for DNA bending by bZIP proteins. , 1997, Biochemistry.

[2]  S. Swaminathan,et al.  Investigation of domain structure in proteins via molecular dynamics simulation: application to HIV-1 protease dimer , 1991 .

[3]  A. Rich,et al.  Asymmetric lateral distribution of unshielded phosphate groups in nucleosomal DNA and its role in DNA bending. , 1979, Proceedings of the National Academy of Sciences of the United States of America.

[4]  B. Matthews,et al.  Protein flexibility and adaptability seen in 25 crystal forms of T4 lysozyme. , 1995, Journal of molecular biology.

[5]  J. Perona,et al.  Role of protein-induced bending in the specificity of DNA recognition: crystal structure of EcoRV endonuclease complexed with d(AAAGAT) + d(ATCTT). , 1998, Journal of molecular biology.

[6]  Collaborative Computational,et al.  The CCP4 suite: programs for protein crystallography. , 1994, Acta crystallographica. Section D, Biological crystallography.

[7]  R. S. Spolar,et al.  Coupling of local folding to site-specific binding of proteins to DNA. , 1994, Science.

[8]  R. Lavery,et al.  Defining the structure of irregular nucleic acids: conventions and principles. , 1989, Journal of biomolecular structure & dynamics.

[9]  S. Harrison,et al.  Differing roles for zinc fingers in DNA recognition: structure of a six-finger transcription factor IIIA complex. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[10]  R. Bryan,et al.  The crystal structure of EcoRV endonuclease and of its complexes with cognate and non-cognate DNA fragments. , 1993 .

[11]  S. Halford,et al.  Rapid reaction analysis of the catalytic cycle of the EcoRV restriction endonuclease. , 1995, Biochemistry.

[12]  Axel T. Brunger,et al.  Free R value: cross-validation in crystallography. , 1997 .

[13]  C. Banner,et al.  The cleavage site for the restriction endonuclease EcoRV is 5'-GAT/ATC-3'. , 1984, Gene.

[14]  J. Perona,et al.  Metal ion-mediated substrate-assisted catalysis in type II restriction endonucleases. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[15]  T. Oelgeschläger,et al.  A site-directed mutagenesis study to identify amino acid residues involved in the catalytic function of the restriction endonuclease EcoRV. , 1992, Biochemistry.

[16]  M. Karplus,et al.  Crystallographic R Factor Refinement by Molecular Dynamics , 1987, Science.

[17]  C. Hunter,et al.  DNA base-stacking interactions: a comparison of theoretical calculations with oligonucleotide X-ray crystal structures. , 1997, Journal of molecular biology.

[18]  G. Schulz,et al.  Movie of the structural changes during a catalytic cycle of nucleoside monophosphate kinases. , 1995, Structure.

[19]  John J. Perona,et al.  Structural and energetic origins of indirect readout in site-specific DNA cleavage by a restriction endonuclease , 1998, Nature Structural Biology.

[20]  B. Lee,et al.  The interpretation of protein structures: estimation of static accessibility. , 1971, Journal of molecular biology.

[21]  John W. R. Schwabe,et al.  The crystal structure of the estrogen receptor DNA-binding domain bound to DNA: How receptors discriminate between their response elements , 1993, Cell.

[22]  A. Aggarwal.  Crystallization of DNA binding proteins with oligodeoxynucleotides. , 1990, Methods.

[23]  V. Zhurkin,et al.  DNA sequence-dependent deformability deduced from protein-DNA crystal complexes. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[24]  J. N. Mark Glover,et al.  Crystal structure of the heterodimeric bZIP transcription factor c-Fos–c-Jun bound to DNA , 1995, Nature.

[25]  J. Berg,et al.  A 2.2 Å resolution crystal structure of a designed zinc finger protein bound to DNA , 1996, Nature Structural Biology.

[26]  L. J. Maher,et al.  DNA bending by asymmetric phosphate neutralization. , 1994, Science.

[27]  J. Schwabe,et al.  Towards an understanding of protein-DNA recognition. , 1996, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.

[28]  A. Jeltsch,et al.  Probing the Indirect Readout of the Restriction Enzyme EcoRV , 1996, The Journal of Biological Chemistry.

[29]  F. Winkler,et al.  Mg2+ binding to the active site of EcoRV endonuclease: a crystallographic study of complexes with substrate and product DNA at 2 A resolution. , 1995, Biochemistry.

[30]  J. Perona,et al.  Conformational transitions and structural deformability of EcoRV endonuclease revealed by crystallographic analysis. , 1997, Journal of molecular biology.

[31]  Tom Maniatis,et al.  Transcriptional activation: A complex puzzle with few easy pieces , 1994, Cell.

[32]  B C Finzel,et al.  Mastering the LORE of protein structure. , 1995, Acta crystallographica. Section D, Biological crystallography.

[33]  H. Berman,et al.  New parameters for the refinement of nucleic acid-containing structures. , 1996, Acta crystallographica. Section D, Biological crystallography.

[34]  F. Brooks,et al.  Force display in molecular docking , 1990 .