2j6t
From Proteopedia
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==Overview== | ==Overview== | ||
| - | 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 .. | + | 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 Structure== | ==About this Structure== | ||
| - | 2J6T is a | + | 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] Structure known Active Site: AC1. Full crystallographic information is available from [http://ispc.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://ispc.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Mon Nov 5 12:51:31 2007'' |
Revision as of 10:46, 5 November 2007
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TERNARY COMPLEX OF SULFOLOBUS SOLFATARICUS DPO4 DNA POLYMERASE, O6-METHYLGUANINE MODIFIED DNA, AND DATP.
Overview
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 Structure
2J6T is a Single protein structure of sequence from Sulfolobus solfataricus with CA and DTP as ligands. Active as DNA-directed DNA polymerase, with EC number 2.7.7.7 Structure known Active Site: AC1. Full crystallographic information is available from OCA.
Reference
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
Page seeded by OCA on Mon Nov 5 12:51:31 2007
Categories: 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
