2j6s | pdb_00002j6s

TERNARY COMPLEX OF SULFOLOBUS SOLFATARICUS DPO4 DNA POLYMERASE, O6-METHYLGUANINE MODIFIED DNA, AND DATP.

spinqualitylabelsall models 2j6s, resolution 2.50Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 2j6s is a 3 chain structure with sequence from Sulfolobus solfataricus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: CA, DTP NonStd Res: 6OG 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 Activity: DNA-directed DNA polymerase, with EC number 2.7.7.7 Resources: FirstGlance, OCA, RCSB, PDBsum Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMed 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. See Also DNA polymerase

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