3bdp: Difference between revisions
New page: left|200px<br /><applet load="3bdp" size="450" color="white" frame="true" align="right" spinBox="true" caption="3bdp, resolution 1.90Å" /> '''DNA POLYMERASE I/DNA... |
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[[Image:3bdp.gif|left|200px]]<br /><applet load="3bdp" size=" | [[Image:3bdp.gif|left|200px]]<br /><applet load="3bdp" size="350" color="white" frame="true" align="right" spinBox="true" | ||
caption="3bdp, resolution 1.90Å" /> | caption="3bdp, resolution 1.90Å" /> | ||
'''DNA POLYMERASE I/DNA COMPLEX'''<br /> | '''DNA POLYMERASE I/DNA COMPLEX'''<br /> | ||
==Overview== | ==Overview== | ||
DNA polymerases copy DNA templates with remarkably high fidelity, checking | DNA polymerases copy DNA templates with remarkably high fidelity, checking for correct base-pair formation both at nucleotide insertion and at subsequent DNA extension steps. Despite extensive biochemical, genetic and structural studies, the mechanism by which nucleotides are correctly incorporated is not known. Here we present high-resolution crystal structures of a thermostable bacterial (Bacillus stearothermophilus) DNA polymerase I large fragments with DNA primer templates bound productively at the polymerase active site. The active site retains catalytic activity, allowing direct observation of the products of several rounds of nucleotide incorporation. The polymerase also retains its ability to discriminate between correct and incorrectly paired nucleotides in the crystal. Comparison of the structures of successively translocated complexes allows the structural features for the sequence-independent molecular recognition of correctly formed base pairs to be deduced unambiguously. These include extensive interactions with the first four to five base pairs in the minor groove, location of the terminal base pair in a pocket of excellent steric complementarity favouring correct base-pair formation, and a conformational switch from B-form to underwound A-form DNA at the polymerase active site. | ||
==About this Structure== | ==About this Structure== | ||
3BDP is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus] with SO4 as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [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] Full crystallographic information is available from [http:// | 3BDP is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus] with <scene name='pdbligand=SO4:'>SO4</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [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] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BDP OCA]. | ||
==Reference== | ==Reference== | ||
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[[Category: Geobacillus stearothermophilus]] | [[Category: Geobacillus stearothermophilus]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
[[Category: Beese, L | [[Category: Beese, L S.]] | ||
[[Category: Kiefer, J | [[Category: Kiefer, J R.]] | ||
[[Category: Mao, C.]] | [[Category: Mao, C.]] | ||
[[Category: SO4]] | [[Category: SO4]] | ||
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[[Category: complex (nucleotidyltransferase/dna)]] | [[Category: complex (nucleotidyltransferase/dna)]] | ||
''Page seeded by [http:// | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 19:04:58 2008'' | ||
Revision as of 20:04, 21 February 2008
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DNA POLYMERASE I/DNA COMPLEX
OverviewOverview
DNA polymerases copy DNA templates with remarkably high fidelity, checking for correct base-pair formation both at nucleotide insertion and at subsequent DNA extension steps. Despite extensive biochemical, genetic and structural studies, the mechanism by which nucleotides are correctly incorporated is not known. Here we present high-resolution crystal structures of a thermostable bacterial (Bacillus stearothermophilus) DNA polymerase I large fragments with DNA primer templates bound productively at the polymerase active site. The active site retains catalytic activity, allowing direct observation of the products of several rounds of nucleotide incorporation. The polymerase also retains its ability to discriminate between correct and incorrectly paired nucleotides in the crystal. Comparison of the structures of successively translocated complexes allows the structural features for the sequence-independent molecular recognition of correctly formed base pairs to be deduced unambiguously. These include extensive interactions with the first four to five base pairs in the minor groove, location of the terminal base pair in a pocket of excellent steric complementarity favouring correct base-pair formation, and a conformational switch from B-form to underwound A-form DNA at the polymerase active site.
About this StructureAbout this Structure
3BDP is a Single protein structure of sequence from Geobacillus stearothermophilus with as ligand. Active as DNA-directed DNA polymerase, with EC number 2.7.7.7 Full crystallographic information is available from OCA.
ReferenceReference
Visualizing DNA replication in a catalytically active Bacillus DNA polymerase crystal., Kiefer JR, Mao C, Braman JC, Beese LS, Nature. 1998 Jan 15;391(6664):304-7. PMID:9440698
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