1nk5
From Proteopedia
(New page: 200px<br /><applet load="1nk5" size="450" color="white" frame="true" align="right" spinBox="true" caption="1nk5, resolution 2.10Å" /> '''ADENINE-ADENINE MISM...) |
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| - | [[Image:1nk5.jpg|left|200px]]<br /><applet load="1nk5" size=" | + | [[Image:1nk5.jpg|left|200px]]<br /><applet load="1nk5" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1nk5, resolution 2.10Å" /> | caption="1nk5, resolution 2.10Å" /> | ||
'''ADENINE-ADENINE MISMATCH AT THE POLYMERASE ACTIVE SITE'''<br /> | '''ADENINE-ADENINE MISMATCH AT THE POLYMERASE ACTIVE SITE'''<br /> | ||
==Overview== | ==Overview== | ||
| - | Accurate DNA replication is essential for genomic stability. One mechanism | + | Accurate DNA replication is essential for genomic stability. One mechanism by which high-fidelity DNA polymerases maintain replication accuracy involves stalling of the polymerase in response to covalent incorporation of mismatched base pairs, thereby favoring subsequent mismatch excision. Some polymerases retain a "short-term memory" of replication errors, responding to mismatches up to four base pairs in from the primer terminus. Here we a present a structural characterization of all 12 possible mismatches captured at the growing primer terminus in the active site of a polymerase. Our observations suggest four mechanisms that lead to mismatch-induced stalling of the polymerase. Furthermore, we have observed the effects of extending a mismatch up to six base pairs from the primer terminus and find that long-range distortions in the DNA transmit the presence of the mismatch back to the enzyme active site, suggesting the structural basis for the short-term memory of replication errors. |
==About this Structure== | ==About this Structure== | ||
| - | 1NK5 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus] with SUC, MG and SO4 as [http://en.wikipedia.org/wiki/ligands ligands]. 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:// | + | 1NK5 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus] with <scene name='pdbligand=SUC:'>SUC</scene>, <scene name='pdbligand=MG:'>MG</scene> and <scene name='pdbligand=SO4:'>SO4</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. 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=1NK5 OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Geobacillus stearothermophilus]] | [[Category: Geobacillus stearothermophilus]] | ||
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
| - | [[Category: Beese, L | + | [[Category: Beese, L S.]] |
| - | [[Category: Johnson, S | + | [[Category: Johnson, S J.]] |
[[Category: MG]] | [[Category: MG]] | ||
[[Category: SO4]] | [[Category: SO4]] | ||
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[[Category: protein-dna complex]] | [[Category: protein-dna complex]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:06:56 2008'' |
Revision as of 12:07, 21 February 2008
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ADENINE-ADENINE MISMATCH AT THE POLYMERASE ACTIVE SITE
Overview
Accurate DNA replication is essential for genomic stability. One mechanism by which high-fidelity DNA polymerases maintain replication accuracy involves stalling of the polymerase in response to covalent incorporation of mismatched base pairs, thereby favoring subsequent mismatch excision. Some polymerases retain a "short-term memory" of replication errors, responding to mismatches up to four base pairs in from the primer terminus. Here we a present a structural characterization of all 12 possible mismatches captured at the growing primer terminus in the active site of a polymerase. Our observations suggest four mechanisms that lead to mismatch-induced stalling of the polymerase. Furthermore, we have observed the effects of extending a mismatch up to six base pairs from the primer terminus and find that long-range distortions in the DNA transmit the presence of the mismatch back to the enzyme active site, suggesting the structural basis for the short-term memory of replication errors.
About this Structure
1NK5 is a Protein complex structure of sequences from Geobacillus stearothermophilus with , and as ligands. Active as DNA-directed DNA polymerase, with EC number 2.7.7.7 Full crystallographic information is available from OCA.
Reference
Structures of mismatch replication errors observed in a DNA polymerase., Johnson SJ, Beese LS, Cell. 2004 Mar 19;116(6):803-16. PMID:15035983
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