2imw: Difference between revisions
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|PDB= 2imw |SIZE=350|CAPTION= <scene name='initialview01'>2imw</scene>, resolution 2.050Å | |PDB= 2imw |SIZE=350|CAPTION= <scene name='initialview01'>2imw</scene>, resolution 2.050Å | ||
|SITE= | |SITE= | ||
|LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DAD:2 | |LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DAD:2',3'-DIDEOXYADENOSINE-5'-TRIPHOSPHATE'>DAD</scene> and <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene> | ||
|ACTIVITY= [http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] | |ACTIVITY= [http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] | ||
|GENE= dbin ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2287 Sulfolobus solfataricus]) | |GENE= dbin ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2287 Sulfolobus solfataricus]) | ||
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[[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 | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 23 15:21:36 2008'' | ||
Revision as of 13:21, 23 March 2008
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| 2imw, resolution 2.050Å | |||||||||||||
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| Ligands: | CA, DAD and EDO | ||||||||||||
| Gene: | dbin (Sulfolobus solfataricus) | ||||||||||||
| Activity: | DNA-directed DNA polymerase, with EC number 2.7.7.7 | ||||||||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||||||||
Mechanism of Template-Independent Nucleotide Incorporation Catalyzed by a Template-Dependent DNA Polymerase
Overview
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.
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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