1tkd: Difference between revisions

Revision as of 10:03, 3 May 2008

T7 DNA polymerase ternary complex with 8 oxo guanosine and dCMP 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

1TKD 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 Page seeded by OCA on Sat May 3 10:03:25 2008

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
 [[Image:1tkd.gif|left|200px]]
- {{Structure
+<!--
-|PDB= 1tkd |SIZE=350|CAPTION= <scene name='initialview01'>1tkd</scene>, resolution 2.49&Aring;
+The line below this paragraph, containing "STRUCTURE_1tkd", creates the "Structure Box" on the page.
-|SITE=
+You may change the PDB parameter (which sets the PDB file loaded into the applet)
-|LIGAND= <scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</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=DOC:2&#39;,3&#39;-DIDEOXYCYTIDINE-5&#39;-MONOPHOSPHATE'>DOC</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>
+or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-|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>
+or leave the SCENE parameter empty for the default display.
-|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=
+{{STRUCTURE_1tkd|  PDB=1tkd  |  SCENE=  }}
-|RELATEDENTRY=[[1tk8|1TK8]], [[1tk5|1TK5]], [[1tk0|1TK0]], [[1t8e|1T8E]]
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1tkd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tkd OCA], [http://www.ebi.ac.uk/pdbsum/1tkd PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1tkd RCSB]</span>
-}}
 '''T7 DNA polymerase ternary complex with 8 oxo guanosine and dCMP at the elongation site'''
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 [[Category: Kunkel, T A.]]
 [[Category: 8-oxoguanosine dna polymerase]]
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 10:03:25 2008''
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 23:57:17 2008''