Conformational flexibility in T4 endonuclease VII revealed by crystallography: Implications for substrate binding and cleavage

Journal of Molecular Biology

Volumn 308, Issue 2, 2001, Pages 311-323

  Raaijmakers, Hans ^a   Törö, Imre ^a   Birkenbihl, Rainer ^b   Kemper, Börries ^b   Suck, Dietrich ^a  

^a EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

^b UNIVERSITY OF COLOGNE   (Germany)

Author keywords

Conformational flexibility; Endonuclease VII; Enzymatic mechanism; High resolution X ray structure; Mg dependent nucleases

Indexed keywords

ENDONUCLEASE; ENDONUCLEASE VII; MAGNESIUM; METAL ION; MUTANT PROTEIN; SULFATE; UNCLASSIFIED DRUG;

ARTICLE; BACTERIOPHAGE T4; CARBOXY TERMINAL SEQUENCE; CATALYSIS; CRYSTALLOGRAPHY; DIMERIZATION; DNA BINDING; ENZYME CONFORMATION; ENZYME STRUCTURE; ENZYME SUBSTRATE; HYDROPHOBICITY; NONHUMAN; PRIORITY JOURNAL; SERRATIA;

SERRATIA;

EID: 0035957509     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.2001.4592     Document Type: Article

References (46)

1. Atomic structure of the RuvC resolvase: A Holliday junction specific endonuclease from E. coli
2. Model for the interaction of the DNA junctions and resolving enzymes
3. Localization and characterization of the dimerization domain of Holliday-structure resolving endonuclease VII
4. Endonuclease VII has two DNA-binding sites each composed from one N- and one C terminus provided by different subunits of the protein dimer
5. The CCP4 suite: Programs for protein crystallography
6. "dm": An automated procedure for phase improvement by density modification
7. DNA binding and cleavage by the nuclear intron-encoded homing endonuclease I-PpoI
8. Cleavage experiments with deoxythymidine 3′,5′-bis-(p-nitrophenylphosphate) suggest that the homing endonuclease I-PpoI follows the same mechanism of phosphodiester bond hydrolysis as the non-specific Serratia nuclease
9. T4 endonuclease VII: Importance of a histidine-aspartate cluster within the zinc-binding domain
10. Near simultaneous DNA cleavage by the subunits of the junction resolving enzyme T4 endonuclease VII
11. Improved large scale preparation of phage T4 endonuclease VII overexpressed in E. coli
12. Identification of amino acids of endonuclease VII essential for binding and cleavage of cruciform DNA
13. The role of T4-bacteriophage endonuclease VII in autocorrection of mismatched regions
14. An apyrimidinic site kinks DNA and triggers incision by endonuclease VII of phage T4
15. TLSANL: TLS parameter analysis program for segmented anisotropic refinement of macromolecular structures
16. Errors in protein structures
17. Improved methods for building protein models in electron density maps and the location of errors in these models
18. A solution for the best rotation to relate two sets of vectors
19. Three dimensional structure of ribonuclease H. from E. coli
20. Branched DNA resolving enzymes
21. Function of gene 49 of bacteriophage T4 II. Analysis of intracellular development and the structure of very fast sedimenting DNA
22. Resolution of DNA secondary structures by endonuclease VII (EndoVII) from phage T4
23. Structural and mechanistic basis of immunity toward endonuclease colicins
24. Phi/psi-chology: Ramachandran revisited
25. MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures
26. Structural parsimony in endonuclease active sites: Should the number of homing endonuclease families be redefined?
27. Automated refinement of protein models
28. PROCHECK: A program to check the stereochemical quality of protein structures
29. The interpretation of protein structures: Estimation of static accessibility
30. Raster3D: Photorealistic molecular graphics
31. 2.1 Å structure of Serratia endonuclease suggests a mechanism for binding to double-stranded DNA
32. T4 endonuclease VII cleaves Holliday structures
33. Efficient anisotropic refinement of Macromolecular structures using FFT
34. AMoRe: An automated package for molecular replacement
35. Processing of X-ray diffraction data collected in oscillation mode
36. T4 endonuclease VII resolves cruciform DNA with nick and counter nick and its activity is directed by its local nucleotide sequence
37. X-ray structure of T4 endonuclease VII: A DNA junction resolvase with novel fold and unusual domain swapped architecture
38. Stereochemical criteria for polypeptide and protein chain conformations. II. Allowed conformations for a pair of peptide units
39. On the rigid-body motion of molecules in crystals
40. The RuvC protein dimer resolves Holliday junctions by a dual incision mechanism that involves base-specific contacts
41. Endonuclease VII of phage T4 triggers mismatch correction in vitro
42. X-ray structure of the DNase-I d(GGTATACC)2 complex at 2.3 Å resolution
43. The structure-selectivity and sequence-preference of the junction-resolving enzyme CCE1 of Saccharomyces cerevisiae
44. Recognition and manipulation of branched DNA structure by junction resolving enzymes
45. Use of TLS parameters to model anisotropic displacements in macromolecular refinement
46. Screening for mutations by enzyme mismatch cleavage by T4 endonuclease VII