2ivk: Difference between revisions
No edit summary |
No edit summary |
||
| Line 1: | Line 1: | ||
[[Image:2ivk.gif|left|200px]] | [[Image:2ivk.gif|left|200px]] | ||
<!-- | |||
The line below this paragraph, containing "STRUCTURE_2ivk", creates the "Structure Box" on the page. | |||
You may change the PDB parameter (which sets the PDB file loaded into the applet) | |||
or the SCENE parameter (which sets the initial scene displayed when the page is loaded), | |||
| | or leave the SCENE parameter empty for the default display. | ||
| | --> | ||
{{STRUCTURE_2ivk| PDB=2ivk | SCENE= }} | |||
}} | |||
'''CRYSTAL STRUCTURE OF THE PERIPLASMIC ENDONUCLEASE VVN COMPLEXED WITH A 16-BP DNA''' | '''CRYSTAL STRUCTURE OF THE PERIPLASMIC ENDONUCLEASE VVN COMPLEXED WITH A 16-BP DNA''' | ||
| Line 30: | Line 27: | ||
[[Category: Yang, W J.]] | [[Category: Yang, W J.]] | ||
[[Category: Yuan, H S.]] | [[Category: Yuan, H S.]] | ||
[[Category: | [[Category: Dna cleavage preference]] | ||
[[Category: | [[Category: Dna hydrolysis]] | ||
[[Category: | [[Category: Dnase]] | ||
[[Category: | [[Category: Endonuclease]] | ||
[[Category: | [[Category: Hydrolase]] | ||
[[Category: | [[Category: Protein nucleic acid interaction]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 07:56:25 2008'' | |||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | |||
Revision as of 07:56, 4 May 2008
CRYSTAL STRUCTURE OF THE PERIPLASMIC ENDONUCLEASE VVN COMPLEXED WITH A 16-BP DNA
OverviewOverview
Nonspecific endonucleases hydrolyze DNA without sequence specificity but with sequence preference, however the structural basis for cleavage preference remains elusive. We show here that the nonspecific endonuclease ColE7 cleaves DNA with a preference for making nicks after (at 3'O-side) thymine bases but the periplasmic nuclease Vvn cleaves DNA more evenly with little sequence preference. The crystal structure of the 'preferred complex' of the nuclease domain of ColE7 bound to an 18 bp DNA with a thymine before the scissile phosphate had a more distorted DNA phosphate backbone than the backbones in the non-preferred complexes, so that the scissile phosphate was compositionally closer to the endonuclease active site resulting in more efficient DNA cleavage. On the other hand, in the crystal structure of Vvn in complex with a 16 bp DNA, the DNA phosphate backbone was similar and not distorted in comparison with that of a previously reported complex of Vvn with a different DNA sequence. Taken together these results suggest a general structural basis for the sequence-dependent DNA cleavage catalyzed by nonspecific endonucleases, indicating that nonspecific nucleases could induce DNA to deform to distinctive levels depending on the local sequence leading to different cleavage rates along the DNA chain.
About this StructureAbout this Structure
2IVK is a Protein complex structure of sequences from Vibrio vulnificus. Full crystallographic information is available from OCA.
ReferenceReference
Structural basis for sequence-dependent DNA cleavage by nonspecific endonucleases., Wang YT, Yang WJ, Li CL, Doudeva LG, Yuan HS, Nucleic Acids Res. 2007;35(2):584-94. Epub 2006 Dec 15. PMID:17175542 Page seeded by OCA on Sun May 4 07:56:25 2008