1zyq
From Proteopedia
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|PDB= 1zyq |SIZE=350|CAPTION= <scene name='initialview01'>1zyq</scene>, resolution 2.70Å | |PDB= 1zyq |SIZE=350|CAPTION= <scene name='initialview01'>1zyq</scene>, resolution 2.70Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand= | + | |LIGAND= <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=DAD:2',3'-DIDEOXYADENOSINE-5'-TRIPHOSPHATE'>DAD</scene>, <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</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=MG:MAGNESIUM+ION'>MG</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, fipA, tsnC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli]) |
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[1t7p|1T7P]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1zyq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zyq OCA], [http://www.ebi.ac.uk/pdbsum/1zyq PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1zyq RCSB]</span> | ||
}} | }} | ||
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==About this Structure== | ==About this Structure== | ||
| - | 1ZYQ is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/ | + | 1ZYQ 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=1ZYQ OCA]. |
==Reference== | ==Reference== | ||
A lysine residue in the fingers subdomain of T7 DNA polymerase modulates the miscoding potential of 8-oxo-7,8-dihydroguanosine., Brieba LG, Kokoska RJ, Bebenek K, Kunkel TA, Ellenberger T, Structure. 2005 Nov;13(11):1653-9. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16271888 16271888] | A lysine residue in the fingers subdomain of T7 DNA polymerase modulates the miscoding potential of 8-oxo-7,8-dihydroguanosine., Brieba LG, Kokoska RJ, Bebenek K, Kunkel TA, Ellenberger T, Structure. 2005 Nov;13(11):1653-9. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16271888 16271888] | ||
| - | [[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: DAD]] | ||
| - | [[Category: MG]] | ||
[[Category: 8og]] | [[Category: 8og]] | ||
[[Category: fidelity]] | [[Category: fidelity]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 01:43:25 2008'' |
Revision as of 22:43, 30 March 2008
| |||||||
| , resolution 2.70Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , , , , , | ||||||
| Gene: | 5 (Enterobacteria phage T7), trxA, fipA, tsnC (Escherichia coli) | ||||||
| Activity: | DNA-directed DNA polymerase, with EC number 2.7.7.7 | ||||||
| Related: | 1T7P
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
T7 DNA polymerase in complex with 8oG and incoming ddATP
Overview
8-oxo-7,8-dihydroguanosine (8oG) is a highly mutagenic DNA lesion that stably pairs with adenosine, forming 8oG(syn).dA(anti) Hoogsteen base pairs. DNA polymerases show different propensities to insert dCMP or dAMP opposite 8oG, but the molecular mechanisms that determine faithful or mutagenic bypass are poorly understood. Here, we report kinetic and structural data providing evidence that, in T7 DNA polymerase, residue Lys536 is responsible for attenuating the miscoding potential of 8oG. The Lys536Ala polymerase shows a significant increase in mutagenic 8oG bypass versus wild-type polymerase, and a crystal structure of the Lys536Ala mutant reveals a closed complex with an 8oG(syn).dATP mismatch in the polymerase active site, in contrast to the unproductive, open complex previously obtained by using wild-type polymerase. We propose that Lys536 acts as a steric and/or electrostatic filter that attenuates the miscoding potential of 8oG by normally interfering with the binding of 8oG in a syn conformation that pairs with dATP.
About this Structure
1ZYQ is a Protein complex structure of sequences from Enterobacteria phage t7 and Escherichia coli. Full crystallographic information is available from OCA.
Reference
A lysine residue in the fingers subdomain of T7 DNA polymerase modulates the miscoding potential of 8-oxo-7,8-dihydroguanosine., Brieba LG, Kokoska RJ, Bebenek K, Kunkel TA, Ellenberger T, Structure. 2005 Nov;13(11):1653-9. PMID:16271888
Page seeded by OCA on Mon Mar 31 01:43:25 2008
