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2j6s
From Proteopedia
| 2j6s, resolution 2.50Å () | |||||||||
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| Ligands: | , | ||||||||
| Non-Standard Residues: | |||||||||
| Activity: | DNA-directed DNA polymerase, with EC number 2.7.7.7 | ||||||||
| Related: | 1jx4, 1jxl, 1n48, 1n56, 1ryr, 1rys, 1s0m, 1s0n, 1s0o, 1s10, 1s97, 1s9f, 2ago, 2agp, 2agq, 2asd, 2asj, 2asl, 2atl, 2au0, 2bq3, 2bqr, 2bqu, 2br0, 2c22, 2c28, 2c2d, 2c2e, 2c2r, 2j6t, 2j6u | ||||||||
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| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||||
Contents |
TERNARY COMPLEX OF SULFOLOBUS SOLFATARICUS DPO4 DNA POLYMERASE, O6-METHYLGUANINE MODIFIED DNA, AND DATP.
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.
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
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
About this Structure
2j6s is a 3 chain structure with sequence from Sulfolobus solfataricus. Full crystallographic information is available from OCA.
See Also
Reference
- Eoff RL, Irimia A, Egli M, Guengerich FP. Sulfolobus solfataricus DNA polymerase Dpo4 is partially inhibited by "wobble" pairing between O6-methylguanine and cytosine, but accurate bypass is preferred. J Biol Chem. 2007 Jan 12;282(2):1456-67. Epub 2006 Nov 14. PMID:17105728 doi:10.1074/jbc.M609661200
Categories: DNA-directed DNA polymerase | Sulfolobus solfataricus | Egli, M. | Eoff, R L. | Guengerich, F P. | Irimia, A. | 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 | Transferase/dna | Translesion dna synthesis
