1tk8: Difference between revisions

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|PDB= 1tk8 |SIZE=350|CAPTION= <scene name='initialview01'>1tk8</scene>, resolution 2.50&Aring;
|PDB= 1tk8 |SIZE=350|CAPTION= <scene name='initialview01'>1tk8</scene>, resolution 2.50&Aring;
|SITE=  
|SITE=  
|LIGAND= <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=D3T:2&#39;,3&#39;-DIDEOXY-THYMIDINE-5&#39;-TRIPHOSPHATE'>D3T</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene> and <scene name='pdbligand=1PE:PENTAETHYLENE GLYCOL'>1PE</scene>
|LIGAND= <scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=2DA:2&#39;,3&#39;-DIDEOXYADENOSINE-5&#39;-MONOPHOSPHATE'>2DA</scene>, <scene name='pdbligand=8OG:8-OXO-2&#39;-DEOXY-GUANOSINE-5&#39;-MONOPHOSPHATE'>8OG</scene>, <scene name='pdbligand=D3T:2&#39;,3&#39;-DIDEOXY-THYMIDINE-5&#39;-TRIPHOSPHATE'>D3T</scene>, <scene name='pdbligand=DA:2&#39;-DEOXYADENOSINE-5&#39;-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2&#39;-DEOXYCYTIDINE-5&#39;-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2&#39;-DEOXYGUANOSINE-5&#39;-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5&#39;-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= Bacteriophage 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])
|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]], [[1tk0|1TK0]], [[1tk5|1TK5]], [[1tkd|1TKD]]
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1tk8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tk8 OCA], [http://www.ebi.ac.uk/pdbsum/1tk8 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1tk8 RCSB]</span>
}}
}}


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==About this Structure==
==About this Structure==
1TK8 is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Bacteriophage_t7 Bacteriophage 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=1TK8 OCA].  
1TK8 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=1TK8 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]]
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[[Category: Kokoska, R J.]]
[[Category: Kokoska, R J.]]
[[Category: Kunkel, T A.]]
[[Category: Kunkel, T A.]]
[[Category: 1PE]]
[[Category: D3T]]
[[Category: MES]]
[[Category: MG]]
[[Category: SO4]]
[[Category: 8-oxoguanosine dna polymerase]]
[[Category: 8-oxoguanosine dna polymerase]]


''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 23 13:45:01 2008''
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 23:57:13 2008''

Revision as of 23:57, 30 March 2008

File:1tk8.gif


PDB ID 1tk8

Drag the structure with the mouse to rotate
, resolution 2.50Å
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, 1TK0, 1TK5, 1TKD


Resources: FirstGlance, OCA, PDBsum, RCSB
Coordinates: save as pdb, mmCIF, xml



T7 DNA polymerase ternary complex with 8 oxo guanosine and dAMP at the elongation site


OverviewOverview

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 StructureAbout this Structure

1TK8 is a Protein complex structure of sequences from Enterobacteria phage t7 and Escherichia coli. Full crystallographic information is available from OCA.

ReferenceReference

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

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