Flexibility in DNA recombination: Structure of the lambda integrase catalytic core

Science

Volumn 276, Issue 5309, 1997, Pages 126-131

  Kwon, Hyock Joo ^a,b   Tirumalai, Radhakrishna ^c   Landy, Arthur ^c   Ellenberger, Tom ^a,b  

^a HARVARD MEDICAL SCHOOL   (United States)

^b HARVARD UNIVERSITY   (United States)

^c BROWN UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CELL DNA; INTEGRASE;

ARTICLE; CATALYSIS; CONTROLLED STUDY; DNA CLEAVAGE; DNA RECOMBINATION; DNA STRAND; ENZYME ACTIVE SITE; MOLECULAR DYNAMICS; NONHUMAN; PRIORITY JOURNAL;

AMINO ACID SEQUENCE; ATTACHMENT SITES, MICROBIOLOGICAL; BACTERIOPHAGE LAMBDA; BINDING SITES; CLONING, MOLECULAR; CONSERVED SEQUENCE; CRYSTALLOGRAPHY, X-RAY; DNA; DNA NUCLEOTIDYLTRANSFERASES; HYDROGEN BONDING; INTEGRASES; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; RECOMBINASES; RECOMBINATION, GENETIC; TYROSINE; VIRUS INTEGRATION;

ARCHAEA;

EID: 0001656001     PISSN: 00368075     EISSN: None     Source Type: Journal    
DOI: 10.1126/science.276.5309.126     Document Type: Article

References (32)

1. B.-J. Bormann, W. J. Knowles, V. T. Marchesi, J. Biol. Chem. 264, 4033 (1989).
2. M. A. Lemmon et al., ibid. 267, 7683 (1992).
3. M. A. Lemmon, J. M. Flanagan, H. R. Treutlein, J. Zhang, D. M. Engelman, Biochemistry 31, 12719 (1992).
4. 13C-separated NOE spectra [E. R. P. Zuiderweg and S. W. Fesik, Biochemistry 28, 6150 (1989); S. M. Pascal et al., J. Magn. Reson. Ser. B 103 197 (1994)] acquired at 600 MHz with mixing times of 20 ms. Six pairs of protons whose minimum intramonomer separations were found to exceed 5.5 Å due to the constraints of α-helical backbone geometry and J coupling-derived side-chain dihedral information, but which nevertheless exhibited intense NOE correlations, were determined as making intermonomer contacts. All other NOE restraints were treated as having arisen from either intra-or intermonomer cross-relaxation [M. Nilges, Proteins 17, 297 (1993)]. A family of 20 structures was calculated with the program X-PLOR [A. T. Brünger, X-PLOR Version 3.1, User's Manual, Yale University (1992)] and a protocol combining distance geometry and simulated annealing [M. Nilges, G. M. Clore, A. M. Gronenbom, FEBS Lett. 229, 317 (1988)]. No symmetry terms were used. A purely repulsive potential was used to limit the closest approach of nonbonded atoms; no attractive van der Waals or electrostatic terms were used. The 20 structures contain no bond length violations greater than 0.025 Å, no bond angle violations greater than 5°, no NOE distance restraint violations greater than 0.5 Å, and no dihedral violations greater than 5°. The average rms deviations for bond lengths, bond angles, impropers NOE distances, and dihedrals were 0.002 Å, 0.379°, 0.239°, 0.070 Å, and 0.38°, respectively. Residues 74 to 91 of the family of structures are subject to an average of eight experimental restraints per residue and exhibit rms deviations from the mean structure of 0.75 Å for all nonhydrogen atoms and 0.40 Å for backbone atoms; the nonhydrogen atoms of the seven residues forming the dimerization interface have an rmsd of 0.50 Å. The structures have an average intermonomer Lennard-Jones (L-J) energy of -25 ± 7 kcal/mol; this L-J energy did not form part of the mixed target function. The experimental restraints and the atomic positions of the family of structures have been deposited at the Brookhaven Protein Databank (accession number 1AFO).
5. 13C-separated NOE spectra [E. R. P. Zuiderweg and S. W. Fesik, Biochemistry 28, 6150 (1989); S. M. Pascal et al., J. Magn. Reson. Ser. B 103 197 (1994)] acquired at 600 MHz with mixing times of 20 ms. Six pairs of protons whose minimum intramonomer separations were found to exceed 5.5 Å due to the constraints of α-helical backbone geometry and J coupling-derived side-chain dihedral information, but which nevertheless exhibited intense NOE correlations, were determined as making intermonomer contacts. All other NOE restraints were treated as having arisen from either intra-or intermonomer cross-relaxation [M. Nilges, Proteins 17, 297 (1993)]. A family of 20 structures was calculated with the program X-PLOR [A. T. Brünger, X-PLOR Version 3.1, User's Manual, Yale University (1992)] and a protocol combining distance geometry and simulated annealing [M. Nilges, G. M. Clore, A. M. Gronenbom, FEBS Lett. 229, 317 (1988)]. No symmetry terms were used. A purely repulsive potential was used to limit the closest approach of nonbonded atoms; no attractive van der Waals or electrostatic terms were used. The 20 structures contain no bond length violations greater than 0.025 Å, no bond angle violations greater than 5°, no NOE distance restraint violations greater than 0.5 Å, and no dihedral violations greater than 5°. The average rms deviations for bond lengths, bond angles, impropers NOE distances, and dihedrals were 0.002 Å, 0.379°, 0.239°, 0.070 Å, and 0.38°, respectively. Residues 74 to 91 of the family of structures are subject to an average of eight experimental restraints per residue and exhibit rms deviations from the mean structure of 0.75 Å for all nonhydrogen atoms and 0.40 Å for backbone atoms; the nonhydrogen atoms of the seven residues forming the dimerization interface have an rmsd of 0.50 Å. The structures have an average intermonomer Lennard-Jones (L-J) energy of -25 ± 7 kcal/mol; this L-J energy did not form part of the mixed target function. The experimental restraints and the atomic positions of the family of structures have been deposited at the Brookhaven Protein Databank (accession number 1AFO).
6. 13C-separated NOE spectra [E. R. P. Zuiderweg and S. W. Fesik, Biochemistry 28, 6150 (1989); S. M. Pascal et al., J. Magn. Reson. Ser. B 103 197 (1994)] acquired at 600 MHz with mixing times of 20 ms. Six pairs of protons whose minimum intramonomer separations were found to exceed 5.5 Å due to the constraints of α-helical backbone geometry and J coupling-derived side-chain dihedral information, but which nevertheless exhibited intense NOE correlations, were determined as making intermonomer contacts. All other NOE restraints were treated as having arisen from either intra-or intermonomer cross-relaxation [M. Nilges, Proteins 17, 297 (1993)]. A family of 20 structures was calculated with the program X-PLOR [A. T. Brünger, X-PLOR Version 3.1, User's Manual, Yale University (1992)] and a protocol combining distance geometry and simulated annealing [M. Nilges, G. M. Clore, A. M. Gronenbom, FEBS Lett. 229, 317 (1988)]. No symmetry terms were used. A purely repulsive potential was used to limit the closest approach of nonbonded atoms; no attractive van der Waals or electrostatic terms were used. The 20 structures contain no bond length violations greater than 0.025 Å, no bond angle violations greater than 5°, no NOE distance restraint violations greater than 0.5 Å, and no dihedral violations greater than 5°. The average rms deviations for bond lengths, bond angles, impropers NOE distances, and dihedrals were 0.002 Å, 0.379°, 0.239°, 0.070 Å, and 0.38°, respectively. Residues 74 to 91 of the family of structures are subject to an average of eight experimental restraints per residue and exhibit rms deviations from the mean structure of 0.75 Å for all nonhydrogen atoms and 0.40 Å for backbone atoms; the nonhydrogen atoms of the seven residues forming the dimerization interface have an rmsd of 0.50 Å. The structures have an average intermonomer Lennard-Jones (L-J) energy of -25 ± 7 kcal/mol; this L-J energy did not form part of the mixed target function. The experimental restraints and the atomic positions of the family of structures have been deposited at the Brookhaven Protein Databank (accession number 1AFO).
7. 13C-separated NOE spectra [E. R. P. Zuiderweg and S. W. Fesik, Biochemistry 28, 6150 (1989); S. M. Pascal et al., J. Magn. Reson. Ser. B 103 197 (1994)] acquired at 600 MHz with mixing times of 20 ms. Six pairs of protons whose minimum intramonomer separations were found to exceed 5.5 Å due to the constraints of α-helical backbone geometry and J coupling-derived side-chain dihedral information, but which nevertheless exhibited intense NOE correlations, were determined as making intermonomer contacts. All other NOE restraints were treated as having arisen from either intra-or intermonomer cross-relaxation [M. Nilges, Proteins 17, 297 (1993)]. A family of 20 structures was calculated with the program X-PLOR [A. T. Brünger, X-PLOR Version 3.1, User's Manual, Yale University (1992)] and a protocol combining distance geometry and simulated annealing [M. Nilges, G. M. Clore, A. M. Gronenbom, FEBS Lett. 229, 317 (1988)]. No symmetry terms were used. A purely repulsive potential was used to limit the closest approach of nonbonded atoms; no attractive van der Waals or electrostatic terms were used. The 20 structures contain no bond length violations greater than 0.025 Å, no bond angle violations greater than 5°, no NOE distance restraint violations greater than 0.5 Å, and no dihedral violations greater than 5°. The average rms deviations for bond lengths, bond angles, impropers NOE distances, and dihedrals were 0.002 Å, 0.379°, 0.239°, 0.070 Å, and 0.38°, respectively. Residues 74 to 91 of the family of structures are subject to an average of eight experimental restraints per residue and exhibit rms deviations from the mean structure of 0.75 Å for all nonhydrogen atoms and 0.40 Å for backbone atoms; the nonhydrogen atoms of the seven residues forming the dimerization interface have an rmsd of 0.50 Å. The structures have an average intermonomer Lennard-Jones (L-J) energy of -25 ± 7 kcal/mol; this L-J energy did not form part of the mixed target function. The experimental restraints and the atomic positions of the family of structures have been deposited at the Brookhaven Protein Databank (accession number 1AFO).
8. 13C-separated NOE spectra [E. R. P. Zuiderweg and S. W. Fesik, Biochemistry 28, 6150 (1989); S. M. Pascal et al., J. Magn. Reson. Ser. B 103 197 (1994)] acquired at 600 MHz with mixing times of 20 ms. Six pairs of protons whose minimum intramonomer separations were found to exceed 5.5 Å due to the constraints of α-helical backbone geometry and J coupling-derived side-chain dihedral information, but which nevertheless exhibited intense NOE correlations, were determined as making intermonomer contacts. All other NOE restraints were treated as having arisen from either intra-or intermonomer cross-relaxation [M. Nilges, Proteins 17, 297 (1993)]. A family of 20 structures was calculated with the program X-PLOR [A. T. Brünger, X-PLOR Version 3.1, User's Manual, Yale University (1992)] and a protocol combining distance geometry and simulated annealing [M. Nilges, G. M. Clore, A. M. Gronenbom, FEBS Lett. 229, 317 (1988)]. No symmetry terms were used. A purely repulsive potential was used to limit the closest approach of nonbonded atoms; no attractive van der Waals or electrostatic terms were used. The 20 structures contain no bond length violations greater than 0.025 Å, no bond angle violations greater than 5°, no NOE distance restraint violations greater than 0.5 Å, and no dihedral violations greater than 5°. The average rms deviations for bond lengths, bond angles, impropers NOE distances, and dihedrals were 0.002 Å, 0.379°, 0.239°, 0.070 Å, and 0.38°, respectively. Residues 74 to 91 of the family of structures are subject to an average of eight experimental restraints per residue and exhibit rms deviations from the mean structure of 0.75 Å for all nonhydrogen atoms and 0.40 Å for backbone atoms; the nonhydrogen atoms of the seven residues forming the dimerization interface have an rmsd of 0.50 Å. The structures have an average intermonomer Lennard-Jones (L-J) energy of -25 ± 7 kcal/mol; this L-J energy did not form part of the mixed target function. The experimental restraints and the atomic positions of the family of structures have been deposited at the Brookhaven Protein Databank (accession number 1AFO).
9. 13C-separated NOE spectra [E. R. P. Zuiderweg and S. W. Fesik, Biochemistry 28, 6150 (1989); S. M. Pascal et al., J. Magn. Reson. Ser. B 103 197 (1994)] acquired at 600 MHz with mixing times of 20 ms. Six pairs of protons whose minimum intramonomer separations were found to exceed 5.5 Å due to the constraints of α-helical backbone geometry and J coupling-derived side-chain dihedral information, but which nevertheless exhibited intense NOE correlations, were determined as making intermonomer contacts. All other NOE restraints were treated as having arisen from either intra-or intermonomer cross-relaxation [M. Nilges, Proteins 17, 297 (1993)]. A family of 20 structures was calculated with the program X-PLOR [A. T. Brünger, X-PLOR Version 3.1, User's Manual, Yale University (1992)] and a protocol combining distance geometry and simulated annealing [M. Nilges, G. M. Clore, A. M. Gronenbom, FEBS Lett. 229, 317 (1988)]. No symmetry terms were used. A purely repulsive potential was used to limit the closest approach of nonbonded atoms; no attractive van der Waals or electrostatic terms were used. The 20 structures contain no bond length violations greater than 0.025 Å, no bond angle violations greater than 5°, no NOE distance restraint violations greater than 0.5 Å, and no dihedral violations greater than 5°. The average rms deviations for bond lengths, bond angles, impropers NOE distances, and dihedrals were 0.002 Å, 0.379°, 0.239°, 0.070 Å, and 0.38°, respectively. Residues 74 to 91 of the family of structures are subject to an average of eight experimental restraints per residue and exhibit rms deviations from the mean structure of 0.75 Å for all nonhydrogen atoms and 0.40 Å for backbone atoms; the nonhydrogen atoms of the seven residues forming the dimerization interface have an rmsd of 0.50 Å. The structures have an average intermonomer Lennard-Jones (L-J) energy of -25 ± 7 kcal/mol; this L-J energy did not form part of the mixed target function. The experimental restraints and the atomic positions of the family of structures have been deposited at the Brookhaven Protein Databank (accession number 1AFO).
10. 13C-separated NOE spectra [E. R. P. Zuiderweg and S. W. Fesik, Biochemistry 28, 6150 (1989); S. M. Pascal et al., J. Magn. Reson. Ser. B 103 197 (1994)] acquired at 600 MHz with mixing times of 20 ms. Six pairs of protons whose minimum intramonomer separations were found to exceed 5.5 Å due to the constraints of α-helical backbone geometry and J coupling-derived side-chain dihedral information, but which nevertheless exhibited intense NOE correlations, were determined as making intermonomer contacts. All other NOE restraints were treated as having arisen from either intra-or intermonomer cross-relaxation [M. Nilges, Proteins 17, 297 (1993)]. A family of 20 structures was calculated with the program X-PLOR [A. T. Brünger, X-PLOR Version 3.1, User's Manual, Yale University (1992)] and a protocol combining distance geometry and simulated annealing [M. Nilges, G. M. Clore, A. M. Gronenbom, FEBS Lett. 229, 317 (1988)]. No symmetry terms were used. A purely repulsive potential was used to limit the closest approach of nonbonded atoms; no attractive van der Waals or electrostatic terms were used. The 20 structures contain no bond length violations greater than 0.025 Å, no bond angle violations greater than 5°, no NOE distance restraint violations greater than 0.5 Å, and no dihedral violations greater than 5°. The average rms deviations for bond lengths, bond angles, impropers NOE distances, and dihedrals were 0.002 Å, 0.379°, 0.239°, 0.070 Å, and 0.38°, respectively. Residues 74 to 91 of the family of structures are subject to an average of eight experimental restraints per residue and exhibit rms deviations from the mean structure of 0.75 Å for all nonhydrogen atoms and 0.40 Å for backbone atoms; the nonhydrogen atoms of the seven residues forming the dimerization interface have an rmsd of 0.50 Å. The structures have an average intermonomer Lennard-Jones (L-J) energy of -25 ± 7 kcal/mol; this L-J energy did not form part of the mixed target function. The experimental restraints and the atomic positions of the family of structures have been deposited at the Brookhaven Protein Databank (accession number 1AFO).
11. 13C-separated NOE spectra [E. R. P. Zuiderweg and S. W. Fesik, Biochemistry 28, 6150 (1989); S. M. Pascal et al., J. Magn. Reson. Ser. B 103 197 (1994)] acquired at 600 MHz with mixing times of 20 ms. Six pairs of protons whose minimum intramonomer separations were found to exceed 5.5 Å due to the constraints of α-helical backbone geometry and J coupling-derived side-chain dihedral information, but which nevertheless exhibited intense NOE correlations, were determined as making intermonomer contacts. All other NOE restraints were treated as having arisen from either intra-or intermonomer cross-relaxation [M. Nilges, Proteins 17, 297 (1993)]. A family of 20 structures was calculated with the program X-PLOR [A. T. Brünger, X-PLOR Version 3.1, User's Manual, Yale University (1992)] and a protocol combining distance geometry and simulated annealing [M. Nilges, G. M. Clore, A. M. Gronenbom, FEBS Lett. 229, 317 (1988)]. No symmetry terms were used. A purely repulsive potential was used to limit the closest approach of nonbonded atoms; no attractive van der Waals or electrostatic terms were used. The 20 structures contain no bond length violations greater than 0.025 Å, no bond angle violations greater than 5°, no NOE distance restraint violations greater than 0.5 Å, and no dihedral violations greater than 5°. The average rms deviations for bond lengths, bond angles, impropers NOE distances, and dihedrals were 0.002 Å, 0.379°, 0.239°, 0.070 Å, and 0.38°, respectively. Residues 74 to 91 of the family of structures are subject to an average of eight experimental restraints per residue and exhibit rms deviations from the mean structure of 0.75 Å for all nonhydrogen atoms and 0.40 Å for backbone atoms; the nonhydrogen atoms of the seven residues forming the dimerization interface have an rmsd of 0.50 Å. The structures have an average intermonomer Lennard-Jones (L-J) energy of -25 ± 7 kcal/mol; this L-J energy did not form part of the mixed target function. The experimental restraints and the atomic positions of the family of structures have been deposited at the Brookhaven Protein Databank (accession number 1AFO).
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32. We thank R. B. Hill, J. R. Tolman, I. T. Arkin, and M. A. Lemmon for assistance and encouragement and D. Jeruzalmi, J. L. Popot, C. E. Rogge, W. P. Russ, and S. C. Stallings for critical evaluations of the manuscript and figures. Pulse sequences provided by L. E. Kay are gratefully acknowledged. Supported by NIH grant P01 GM54160 and NSF grant MCB-9406983.