1tk0
From Proteopedia
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|PDB= 1tk0 |SIZE=350|CAPTION= <scene name='initialview01'>1tk0</scene>, resolution 2.30Å | |PDB= 1tk0 |SIZE=350|CAPTION= <scene name='initialview01'>1tk0</scene>, resolution 2.30Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand= | + | |LIGAND= <scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=8OG:8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE'>8OG</scene>, <scene name='pdbligand=DA:2'-DEOXYADENOSINE-5'-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DCT:2',3'-DIDEOXYCYTIDINE+5'-TRIPHOSPHATE'>DCT</scene>, <scene name='pdbligand=DDG:2',3'-DIDEOXY-GUANOSINE-5'-MONOPHOSPHATE'>DDG</scene>, <scene name='pdbligand=DG:2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5'-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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= 5 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id= | + | |GENE= 5 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10760 Enterobacteria phage T7]), TRXA, TSNC, FIPA, B3781, C4701, Z5291, ECS4714, STM3915, STMD1.75, STY3639, T3381, SF3854, S3905 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli]) |
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[1t8e|1T8E]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1tk0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tk0 OCA], [http://www.ebi.ac.uk/pdbsum/1tk0 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1tk0 RCSB]</span> | ||
}} | }} | ||
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==About this Structure== | ==About this Structure== | ||
| - | 1TK0 is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/ | + | 1TK0 is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t7 Enterobacteria phage t7] and [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TK0 OCA]. |
==Reference== | ==Reference== | ||
Structural basis for the dual coding potential of 8-oxoguanosine by a high-fidelity DNA polymerase., Brieba LG, Eichman BF, Kokoska RJ, Doublie S, Kunkel TA, Ellenberger T, EMBO J. 2004 Sep 1;23(17):3452-61. Epub 2004 Aug 5. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15297882 15297882] | Structural basis for the dual coding potential of 8-oxoguanosine by a high-fidelity DNA polymerase., Brieba LG, Eichman BF, Kokoska RJ, Doublie S, Kunkel TA, Ellenberger T, EMBO J. 2004 Sep 1;23(17):3452-61. Epub 2004 Aug 5. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15297882 15297882] | ||
| - | [[Category: Bacteriophage t7]] | ||
[[Category: DNA-directed DNA polymerase]] | [[Category: DNA-directed DNA polymerase]] | ||
| + | [[Category: Enterobacteria phage t7]] | ||
[[Category: Escherichia coli]] | [[Category: Escherichia coli]] | ||
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
| Line 30: | Line 33: | ||
[[Category: Kokoska, R J.]] | [[Category: Kokoska, R J.]] | ||
[[Category: Kunkel, T A.]] | [[Category: Kunkel, T A.]] | ||
| - | [[Category: 1PE]] | ||
| - | [[Category: DCT]] | ||
| - | [[Category: MES]] | ||
| - | [[Category: MG]] | ||
| - | [[Category: SO4]] | ||
[[Category: 8 oxo guanosine]] | [[Category: 8 oxo guanosine]] | ||
[[Category: dna polymerase]] | [[Category: dna polymerase]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 23 | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 23:57:08 2008'' |
Revision as of 20:57, 30 March 2008
| |||||||
| , resolution 2.30Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , , , , , , , , | ||||||
| Gene: | 5 (Enterobacteria phage T7), TRXA, TSNC, FIPA, B3781, C4701, Z5291, ECS4714, STM3915, STMD1.75, STY3639, T3381, SF3854, S3905 (Escherichia coli) | ||||||
| Activity: | DNA-directed DNA polymerase, with EC number 2.7.7.7 | ||||||
| Related: | 1T8E
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
T7 DNA polymerase ternary complex with 8 oxo guanosine and ddCTP at the insertion site
Overview
Accurate DNA replication involves polymerases with high nucleotide selectivity and proofreading activity. We show here why both fidelity mechanisms fail when normally accurate T7 DNA polymerase bypasses the common oxidative lesion 8-oxo-7, 8-dihydro-2'-deoxyguanosine (8oG). The crystal structure of the polymerase with 8oG templating dC insertion shows that the O8 oxygen is tolerated by strong kinking of the DNA template. A model of a corresponding structure with dATP predicts steric and electrostatic clashes that would reduce but not eliminate insertion of dA. The structure of a postinsertional complex shows 8oG(syn).dA (anti) in a Hoogsteen-like base pair at the 3' terminus, and polymerase interactions with the minor groove surface of the mismatch that mimic those with undamaged, matched base pairs. This explains why translesion synthesis is permitted without proofreading of an 8oG.dA mismatch, thus providing insight into the high mutagenic potential of 8oG.
About this Structure
1TK0 is a Protein complex structure of sequences from Enterobacteria phage t7 and Escherichia coli. Full crystallographic information is available from OCA.
Reference
Structural basis for the dual coding potential of 8-oxoguanosine by a high-fidelity DNA polymerase., Brieba LG, Eichman BF, Kokoska RJ, Doublie S, Kunkel TA, Ellenberger T, EMBO J. 2004 Sep 1;23(17):3452-61. Epub 2004 Aug 5. PMID:15297882
Page seeded by OCA on Sun Mar 30 23:57:08 2008
