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1nkb
From Proteopedia
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|PDB= 1nkb |SIZE=350|CAPTION= <scene name='initialview01'>1nkb</scene>, resolution 2.00Å | |PDB= 1nkb |SIZE=350|CAPTION= <scene name='initialview01'>1nkb</scene>, resolution 2.00Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand= | + | |LIGAND= <scene name='pdbligand=DA:2'-DEOXYADENOSINE-5'-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5'-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=SUC:SUCROSE'>SUC</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= <span class='plainlinks'>[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] </span> |
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[1njw|1NJW]], [[1njx|1NJX]], [[1njy|1NJY]], [[1njz|1NJZ]], [[1nk0|1NK0]], [[1nk4|1NK4]], [[1nk5|1NK5]], [[1nk6|1NK6]], [[1nk7|1NK7]], [[1nk8|1NK8]], [[1nk9|1NK9]], [[1nkc|1NKC]], [[1nke|1NKE]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1nkb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nkb OCA], [http://www.ebi.ac.uk/pdbsum/1nkb PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1nkb RCSB]</span> | ||
}} | }} | ||
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[[Category: Beese, L S.]] | [[Category: Beese, L S.]] | ||
[[Category: Johnson, S J.]] | [[Category: Johnson, S J.]] | ||
| - | [[Category: MG]] | ||
| - | [[Category: SO4]] | ||
| - | [[Category: SUC]] | ||
[[Category: dna mismatch]] | [[Category: dna mismatch]] | ||
[[Category: dna polymerase i]] | [[Category: dna polymerase i]] | ||
| Line 34: | Line 34: | ||
[[Category: protein-dna complex]] | [[Category: protein-dna complex]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 22:31:32 2008'' |
Revision as of 19:31, 30 March 2008
| |||||||
| , resolution 2.00Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , , , , | ||||||
| Activity: | DNA-directed DNA polymerase, with EC number 2.7.7.7 | ||||||
| Related: | 1NJW, 1NJX, 1NJY, 1NJZ, 1NK0, 1NK4, 1NK5, 1NK6, 1NK7, 1NK8, 1NK9, 1NKC, 1NKE
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
A BACILLUS DNA POLYMERASE I PRODUCT COMPLEX BOUND TO A GUANINE-THYMINE MISMATCH AFTER THREE ROUNDS OF PRIMER EXTENSION, FOLLOWING INCORPORATION OF DCTP, DGTP, AND DTTP.
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
1NKB is a Protein complex structure of sequences from Geobacillus stearothermophilus. 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
Page seeded by OCA on Sun Mar 30 22:31:32 2008
