2j6t: Difference between revisions
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[[Image:2j6t.gif|left|200px]]<br /><applet load="2j6t" size=" | [[Image:2j6t.gif|left|200px]]<br /><applet load="2j6t" size="350" color="white" frame="true" align="right" spinBox="true" | ||
caption="2j6t, resolution 2.60Å" /> | caption="2j6t, resolution 2.60Å" /> | ||
'''TERNARY COMPLEX OF SULFOLOBUS SOLFATARICUS DPO4 DNA POLYMERASE, O6-METHYLGUANINE MODIFIED DNA, AND DATP.'''<br /> | '''TERNARY COMPLEX OF SULFOLOBUS SOLFATARICUS DPO4 DNA POLYMERASE, O6-METHYLGUANINE MODIFIED DNA, AND DATP.'''<br /> | ||
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==About this Structure== | ==About this Structure== | ||
2J6T is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Sulfolobus_solfataricus Sulfolobus solfataricus] with CA and DTP 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] Known structural/functional Site: <scene name='pdbsite=AC1:Ca Binding Site For Chain A'>AC1</scene>. Full crystallographic information is available from [http:// | 2J6T is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Sulfolobus_solfataricus Sulfolobus solfataricus] with <scene name='pdbligand=CA:'>CA</scene> and <scene name='pdbligand=DTP:'>DTP</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] Known structural/functional Site: <scene name='pdbsite=AC1:Ca Binding Site For Chain A'>AC1</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2J6T OCA]. | ||
==Reference== | ==Reference== | ||
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[[Category: translesion dna synthesis]] | [[Category: translesion dna synthesis]] | ||
''Page seeded by [http:// | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 23 14:43:09 2008'' | ||
Revision as of 15:43, 23 January 2008
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TERNARY COMPLEX OF SULFOLOBUS SOLFATARICUS DPO4 DNA POLYMERASE, O6-METHYLGUANINE MODIFIED DNA, AND DATP.
OverviewOverview
We examined the effect of a single O6-methylguanine (O6-MeG) template, residue on catalysis by a model Y family polymerase, Dpo4 from Sulfolobus, solfataricus. Mass spectral analysis of Dpo4-catalyzed extension products, revealed that the enzyme accurately bypasses O6-MeG, with C being the, major product (approximately 70%) and T or A being the minor species, (approximately 20% or approximately 10%, respectively), consistent with, steady-state kinetic parameters. Transient-state kinetic experiments, revealed that kpol, the maximum forward rate constant describing, polymerization, for dCTP incorporation opposite O6-MeG was approximately, 6-fold slower than observed for unmodified G, and no measurable product, was observed for dTTP incorporation in the pre-steady state. The lack of, any structural information regarding how O6-MeG paired in a polymerase, active site led us to perform x-ray crystallographic studies, which show, that "wobble" pairing occurs between C and O6-MeG. A structure containing, T opposite O6-MeG was solved, but much of the ribose and pyrimidine base, density was disordered, in accordance with a much higher Km,dTTP that, drives the difference in efficiency between C and T incorporation. The, more stabilized C:O6-MeG pairing reinforces the importance of hydrogen, bonding with respect to nucleotide selection within a geometrically, tolerant polymerase active site.
About this StructureAbout this Structure
2J6T is a Single protein structure of sequence from Sulfolobus solfataricus with and as ligands. Active as DNA-directed DNA polymerase, with EC number 2.7.7.7 Known structural/functional Site: . Full crystallographic information is available from OCA.
ReferenceReference
Sulfolobus solfataricus DNA polymerase Dpo4 is partially inhibited by "wobble" pairing between O6-methylguanine and cytosine, but accurate bypass is preferred., Eoff RL, Irimia A, Egli M, Guengerich FP, J Biol Chem. 2007 Jan 12;282(2):1456-67. Epub 2006 Nov 14. PMID:17105728
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- DNA-directed DNA polymerase
- Single protein
- Sulfolobus solfataricus
- Egli, M.
- Eoff, R.L.
- Guengerich, F.P.
- Irimia, A.
- CA
- DTP
- Dna damage
- Dna polymerase
- Dna repair
- Dna replication
- Dna-binding
- Dna-directed dna polymerase
- Dpo4
- Magnesium
- Metal-binding
- Mutator protein
- Nucleotidyltransferase
- O6-methylguanine
- Transferase
- Transferase/dna complex
- Translesion dna synthesis