Crystal structure of the 64M-2 antibody Fab fragment in complex with a DNA dT(6-4)T photoproduct formed by ultraviolet radiation

Journal of Molecular Biology

Volumn 299, Issue 3, 2000, Pages 711-723

  Yokoyama, Hideshi ^a   Mizutani, Ryuta ^a   Satow, Yoshinori ^a   Komatsu, Yasuo ^b   Ohtsuka, Eiko ^b   Nikaido, Osamu ^c  

^a UNIVERSITY OF TOKYO   (Japan)

^b HOKKAIDO UNIVERSITY   (Japan)

^c KANAZAWA UNIVERSITY   (Japan)

Author keywords

Antibody; Antigen binding fragment; Crystal structure; DNA (6 4) photoproduct; DNA damage

Indexed keywords

DNA ANTIBODY; IMMUNOGLOBULIN F(AB')2 FRAGMENT; PYRIMIDINE DERIVATIVE; PYRIMIDINONE DERIVATIVE;

ANTIBODY SPECIFICITY; ARTICLE; CRYSTAL STRUCTURE; HUMAN; HUMAN CELL; HYDROGEN BOND; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN DNA BINDING; PROTEIN INTERACTION; STRUCTURE ANALYSIS; ULTRAVIOLET RADIATION;

MURINAE;

EID: 0034625308     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.2000.3772     Document Type: Article

References (56)

1. The Protein Date Bank: A computer-based archival file for macromolecular structures
2. Aromatic-aromatic interaction: A mechanism of protein structure stabilization
3. Crystal structure of the cis-syn photodimer of thymidylyl (3'-5') thymidine cyanoethyl ester
4. Conformations of immunoglobulin hypervariable regions
5. Refined structure of the monoclonal antibody HyHEL-5 with its antigen hen egg-white lysozyme
6. 2 antibody 4D5 and comparison with molecular modeling
7. Side-chain torsional potentials: Effect of dipeptide, protein, and solvent environment
8. DNA repair in bacteria and mammalian cells
9. An autoantibody to single-stranded DNA: Comparison of the three-dimensional structures of the unliganded Fab and a deoxynucleotide-Fab complex
10. Repair of thymine dimers and (6-4) photoproducts in group A xeroderma pigmentosum cell lines harboring a transferred normal chromosome 9
11. Synthesis of a phosphoramidite coupling unit of the pyrimidine (6-4) pyrimidone photoproduct and its incorporation into oligonucleotides
12. 26-10 Fab-digoxin complex: Affinity and specificity due to surface complementarity
13. Crystal and molecular structure of a thymine-thymine adduct
14. The solution-structure of DNA duplex-decamer containing the (6-4) photo-product of thymidylyl(3' → 5')thymidine by NMR and relaxation matrix refinement
15. Characterization of (6-4) photo-product DNA photolyase
16. Specificities and rates of binding anti-(6-4) photoproduct antibody fragments to synthetic thymine photoproducts
17. The role of surface lysines in pyrimidine (6-4) pyrimidone photoproduct binding by a high-affinity antibody
18. PROCHECK: A program to check the stereochemical quality of protein structures
19. The thymine-thymine pyrimidine-pyrimidone(6-4) ultra-violet light photoproduct is highly mutagenic and specifically induces 3' thymine-to-cytosine transitions in Escherichia coli
20. Traitement statistique des erreurs dans la determination des structures cristallines
21. Establishment and characterization of a monoclonal antibody recognizing the Dewar isomers of (6-4)photoproducts
22. One type of gammaturn, rather than the other gives rise to chain-reversal in proteins
23. The biology of the (6-4) photoproduct
24. Three-dimensional structures of the Fab fragment of murine N1G9 antibody from the primary immune response and of its complex with (4-hydroxy-3-nitrophenyl)acetate
25. Conformations of the third hypervariable region in the V(H) domain of immuno-globulins
26. Simultaneous establishment of monoclonal antibodies specific for either cyclobutane pyrimidine dimer or (6-4) photoproduct from the same mouse immunized with ultraviolet-irradiated DNA
27. X-ray structure of T4 endonuclease V: An excision repair enzyme specific for a pyrimidine dimer
28. Antibodies specific for (6-4) DNA photoproducts: Cloning, anti-body modeling and construction of a single-chain Fv derivative
29. Protein folding and association: Insights from the interracial and thermodynamic properties of hydrocarbons
30. Structural invariants of antigen binding: Comparison of immunoglobulin V(L)-V(H) and V(L)-V(L) domain dimers
31. Crystal structure of trp repressor/operator complex at atomic resolution
32. Anatomy of the antibody molecule
33. Crystal structure of DNA photolyase from Escherichia coll
34. New parameters for the refinement of nucleic acid-containing structures
35. Preparation, characterization and crystallization of an antibody Fab fragment that recognizes RNA. Crystal structures of native Fab and three Fab-mononucleotide complexes
36. UV irradiation of nucleic acids: Formation, purification and solution conformational analysis of the '6-4 lesion' of dTpdT
37. Repair deficient human disorders and cancer
38. Some methods for examining the interactions between two molecules
39. Unrestrained molecular dynamics of photodamaged DNA in aqueous solution
40. Immunochemical analyses of nucleic acids
41. Repair by human cell extracts of single (6-4) and cyclobutane thymine-thymine photoproducts in DNA
42. Crystal structure of DNA photolyase from Anacystis nidulans
43. DNA, light, and Dewar pyrimidinones: The structure and biological significance of TpT3
44. Solution-state structure of the Dewar pyrimidinone photoproduct of thymidylyl-(3' → 5')-thymidine
45. Models for the solution state structure of the (6-4) photoproduct of thymidylyl-(3' → 5')-thymidine derived via a distance- and angle-constrained conformation search procedure
46. A new photoreactivating enzyme that specifically repairs ultraviolet light-induced (6-4)photoproducts
47. 31P NMR study of the interactions between oligodeoxynucleotides containing (6-4) photoproduct and Fab fragments of monoclonal antibodies specific for (6-4) photoproduct
48. Atomic model of a pyrimidime dimer excision repair enzyme complexed with a DNA substrate: Structural basis for damaged DNA recognition
49. 1.85 Å structure of anti-fluorescein 4-4 20 Fab
50. β-Turns and their distortions: A proposed new nomenclature
51. Reaction mechanism of (6-4) photoproduct