1t8e: Difference between revisions

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Revision as of 15:15, 20 March 2008

File:1t8e.gif

, resolution 2.54Å

Ligands:

, , , and

Gene:

5, T7DNApolymerase (Bacteriophage T7), trxa, tsnc, fipa, b3781, c4701, z5291,Thioredoxin (Escherichia coli)

Activity:

DNA-directed DNA polymerase, with EC number 2.7.7.7

Coordinates:

save as pdb, mmCIF, xml

T7 DNA Polymerase Ternary Complex with dCTP at the Insertion 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

1T8E is a Protein complex structure of sequences from Bacteriophage 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 Thu Mar 20 14:15:11 2008

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

OCA

@@ Line 1: / Line 1: @@
-[[Image:1t8e.gif|left|200px]]<br /><applet load="1t8e" size="350" color="white" frame="true" align="right" spinBox="true"
+[[Image:1t8e.gif|left|200px]]
-caption="1t8e, resolution 2.54&Aring;" />
-'''T7 DNA Polymerase Ternary Complex with dCTP at the Insertion Site.'''<br />
+ {{Structure
+|PDB= 1t8e |SIZE=350|CAPTION= <scene name='initialview01'>1t8e</scene>, resolution 2.54&Aring;
+|SITE=
+|LIGAND= <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=DCT:2',3'-DIDEOXYCYTIDINE+5'-TRIPHOSPHATE'>DCT</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene> and <scene name='pdbligand=PG4:TETRAETHYLENE GLYCOL'>PG4</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]
+|GENE= 5, T7DNApolymerase ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id= Bacteriophage T7]), trxa, tsnc, fipa, b3781, c4701, z5291,Thioredoxin ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])
+}}
+'''T7 DNA Polymerase Ternary Complex with dCTP at the Insertion Site.'''
 ==Overview==
@@ Line 7: / Line 16: @@
 ==About this Structure==
-T8E is a [http://en.wikipedia.org/wiki/Protein_complex 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] with <scene name='pdbligand=MG:'>MG</scene>, <scene name='pdbligand=SO4:'>SO4</scene>, <scene name='pdbligand=DCT:'>DCT</scene>, <scene name='pdbligand=MES:'>MES</scene> and <scene name='pdbligand=PG4:'>PG4</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=1T8E OCA].
+T8E 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=1T8E 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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=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]]
@@ Line 30: / Line 39: @@
 [[Category: transferase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 15:10:57 2008''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 14:15:11 2008''