2imw: Difference between revisions

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[[Image:2imw.gif|left|200px]]
{{Seed}}
[[Image:2imw.png|left|200px]]


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{{STRUCTURE_2imw|  PDB=2imw  |  SCENE=  }}  
{{STRUCTURE_2imw|  PDB=2imw  |  SCENE=  }}  


'''Mechanism of Template-Independent Nucleotide Incorporation Catalyzed by a Template-Dependent DNA Polymerase'''
===Mechanism of Template-Independent Nucleotide Incorporation Catalyzed by a Template-Dependent DNA Polymerase===




==Overview==
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Numerous template-dependent DNA polymerases are capable of catalyzing template-independent nucleotide additions onto blunt-end DNA. Such non-canonical activity has been hypothesized to increase the genomic hypermutability of retroviruses including human immunodeficiency viruses. Here, we employed pre-steady state kinetics and X-ray crystallography to establish a mechanism for blunt-end additions catalyzed by Sulfolobus solfataricus Dpo4. Our kinetic studies indicated that the first blunt-end dATP incorporation was 80-fold more efficient than the second, and among natural deoxynucleotides, dATP was the preferred substrate due to its stronger intrahelical base-stacking ability. Such base-stacking contributions are supported by the 41-fold higher ground-state binding affinity of a nucleotide analog, pyrene nucleoside 5'-triphosphate, which lacks hydrogen bonding ability but possesses four conjugated aromatic rings. A 2.05 A resolution structure of Dpo4*(blunt-end DNA)*ddATP revealed that the base and sugar of the incoming ddATP, respectively, stack against the 5'-base of the opposite strand and the 3'-base of the elongating strand. This unprecedented base-stacking pattern can be applied to subsequent blunt-end additions only if all incorporated dAMPs are extrahelical, leading to predominantly single non-templated dATP incorporation.
The line below this paragraph, {{ABSTRACT_PUBMED_17095011}}, adds the Publication Abstract to the page
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{{ABSTRACT_PUBMED_17095011}}


==About this Structure==
==About this Structure==
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[[Category: Yang, W.]]
[[Category: Yang, W.]]
[[Category: Blunt end dna y-family polymerase dna replication]]
[[Category: Blunt end dna y-family polymerase dna replication]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 07:40:20 2008''
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 02:43:58 2008''

Revision as of 23:44, 28 July 2008

File:2imw.png

Template:STRUCTURE 2imw

Mechanism of Template-Independent Nucleotide Incorporation Catalyzed by a Template-Dependent DNA Polymerase

Template:ABSTRACT PUBMED 17095011

About this Structure

2IMW is a Single protein structure of sequence from Sulfolobus solfataricus. Full crystallographic information is available from OCA.

Reference

Mechanism of template-independent nucleotide incorporation catalyzed by a template-dependent DNA polymerase., Fiala KA, Brown JA, Ling H, Kshetry AK, Zhang J, Taylor JS, Yang W, Suo Z, J Mol Biol. 2007 Jan 19;365(3):590-602. Epub 2006 Oct 7. PMID:17095011

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