1lv5
From Proteopedia
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| - | [[Image:1lv5.jpg|left|200px]] | + | [[Image:1lv5.jpg|left|200px]] |
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| - | '''Crystal Structure of the Closed Conformation of Bacillus DNA Polymerase I Fragment Bound to DNA and dCTP''' | + | {{Structure |
| + | |PDB= 1lv5 |SIZE=350|CAPTION= <scene name='initialview01'>1lv5</scene>, resolution 1.95Å | ||
| + | |SITE= | ||
| + | |LIGAND= <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene> and <scene name='pdbligand=DCP:2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE'>DCP</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] | ||
| + | |GENE= | ||
| + | }} | ||
| + | |||
| + | '''Crystal Structure of the Closed Conformation of Bacillus DNA Polymerase I Fragment Bound to DNA and dCTP''' | ||
| + | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
| - | 1LV5 is a [ | + | 1LV5 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LV5 OCA]. |
==Reference== | ==Reference== | ||
| - | Processive DNA synthesis observed in a polymerase crystal suggests a mechanism for the prevention of frameshift mutations., Johnson SJ, Taylor JS, Beese LS, Proc Natl Acad Sci U S A. 2003 Apr 1;100(7):3895-900. Epub 2003 Mar 20. PMID:[http:// | + | Processive DNA synthesis observed in a polymerase crystal suggests a mechanism for the prevention of frameshift mutations., Johnson SJ, Taylor JS, Beese LS, Proc Natl Acad Sci U S A. 2003 Apr 1;100(7):3895-900. Epub 2003 Mar 20. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12649320 12649320] |
[[Category: DNA-directed DNA polymerase]] | [[Category: DNA-directed DNA polymerase]] | ||
[[Category: Geobacillus stearothermophilus]] | [[Category: Geobacillus stearothermophilus]] | ||
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[[Category: protein-dna-dntp complex]] | [[Category: protein-dna-dntp complex]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 12:35:34 2008'' |
Revision as of 10:35, 20 March 2008
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| , resolution 1.95Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , and | ||||||
| Activity: | DNA-directed DNA polymerase, with EC number 2.7.7.7 | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal Structure of the Closed Conformation of Bacillus DNA Polymerase I Fragment Bound to DNA and dCTP
Overview
DNA polymerases replicate DNA by adding nucleotides to a growing primer strand while avoiding frameshift and point mutations. Here we present a series of up to six successive replication events that were obtained by extension of a primed template directly in a crystal of the thermostable Bacillus DNA polymerase I. The 6-bp extension involves a 20-A translocation of the DNA duplex, representing the largest molecular movement observed in a protein crystal. In addition, we obtained the structure of a "closed" conformation of the enzyme with a bound triphosphate juxtaposed to a template and a dideoxy-terminated primer by constructing a point mutant that destroys a crystal lattice contact stabilizing the wild-type polymerase in an "open" conformation. Together, these observations allow many of the steps involved in DNA replication to be observed in the same enzyme at near atomic detail. The successive replication events observed directly by catalysis in the crystal confirm the general reaction sequence deduced from observations obtained by using several other polymerases and further refine critical aspects of the known reaction mechanism, and also allow us to propose new features that concern the regulated transfer of the template strand between a preinsertion site and an insertion site. We propose that such regulated transfer is an important element in the prevention of frameshift mutations in high-fidelity DNA polymerases. The ability to observe processive, high-fidelity replication directly in a crystal establishes this polymerase as a powerful model system for mechanistic studies in which the structural consequences of mismatches and DNA adducts are observed.
About this Structure
1LV5 is a Single protein structure of sequence from Geobacillus stearothermophilus. Full crystallographic information is available from OCA.
Reference
Processive DNA synthesis observed in a polymerase crystal suggests a mechanism for the prevention of frameshift mutations., Johnson SJ, Taylor JS, Beese LS, Proc Natl Acad Sci U S A. 2003 Apr 1;100(7):3895-900. Epub 2003 Mar 20. PMID:12649320
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