2ivk: Difference between revisions

Revision as of 18:56, 21 February 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 Thu Feb 21 17:56:28 2008

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OCA

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 ==Overview==
-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.
+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 Structure==
@@ Line 13: / Line 13: @@
 [[Category: Protein complex]]
 [[Category: Vibrio vulnificus]]
-[[Category: Doudeva, L.G.]]
+[[Category: Doudeva, L G.]]
-[[Category: Li, C.L.]]
+[[Category: Li, C L.]]
-[[Category: Wang, Y.T.]]
+[[Category: Wang, Y T.]]
-[[Category: Yang, W.J.]]
+[[Category: Yang, W J.]]
-[[Category: Yuan, H.S.]]
+[[Category: Yuan, H S.]]
 [[Category: dna cleavage preference]]
 [[Category: dna hydrolysis]]
@@ Line 25: / Line 25: @@
 [[Category: protein nucleic acid interactions]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jan 29 20:47:06 2008''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 17:56:28 2008''