2va3 | pdb_00002va3

Complex structure of Sulfolobus solfataricus DPO4 and DNA duplex containing a hydrophobic thymine isostere 2,4-difluorotoluene nucleotide in the template strand

spinqualitylabelsall models 2va3, resolution 2.98Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 2va3 is a 3 chain structure with sequence from Sulso. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: CA, DGT NonStd Res: DFT Related: 2asl, 1s0m, 2jeg, 1rys, 2j6t, 1n56, 2atl, 1jx4, 2c22, 2va2, 1s97, 2agq, 2jej, 2ago, 2asj, 2asd, 1n48, 1jxl, 2bq3, 2uvu, 2j6u, 2agp, 1s0n, 2c2r, 2jef, 1s0o, 2uvw, 2bqr, 2jei, 1s9f, 2au0, 2bqu, 2c28, 2v9w, 2c2e, 1ryr, 2uvv, 2c2d, 2br0, 1s10, 2j6s, 2uvr Activity: DNA-directed DNA polymerase, with EC number 2.7.7.7 Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT 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 The 2,4-difluorotoluene (DFT) analog of thymine has been used extensively to probe the relative importance of shape and hydrogen bonding for correct nucleotide insertion by DNA polymerases. As far as high fidelity (A-class) polymerases are concerned, shape is considered by some as key to incorporation of A(T) opposite T(A) and G(C) opposite C(G). We have carried out a detailed kinetic analysis of in vitro primer extension opposite DFT-containing templates by the trans-lesion (Y-class) DNA polymerase Dpo4 from Sulfolobus solfataricus. Although full-length product formation was observed, steady-state kinetic data show that dATP insertion opposite DFT is greatly inhibited relative to insertion opposite T (approximately 5,000-fold). No products were observed in the pre-steady-state. Furthermore, it is noteworthy that Dpo4 strongly prefers dATP opposite DFT over dGTP (approximately 200-fold) and that the polymerase is able to extend an A:DFT but not a G:DFT pair. We present crystal structures of Dpo4 in complex with DNA duplexes containing the DFT analog, the first for any DNA polymerase. In the structures, template-DFT is either positioned opposite primer-A or -G at the -1 site or is unopposed by a primer base and followed by a dGTP:A mismatch pair at the active site, representative of a -1 frameshift. The three structures provide insight into the discrimination by Dpo4 between dATP and dGTP opposite DFT and its inability to extend beyond a G:DFT pair. Although hydrogen bonding is clearly important for error-free replication by this Y-class DNA polymerase, our work demonstrates that Dpo4 also relies on shape and electrostatics to distinguish between correct and incorrect incoming nucleotide. Structure and activity of Y-class DNA polymerase DPO4 from Sulfolobus solfataricus with templates containing the hydrophobic thymine analog 2,4-difluorotoluene.,Irimia A, Eoff RL, Pallan PS, Guengerich FP, Egli M J Biol Chem. 2007 Dec 14;282(50):36421-33. Epub 2007 Oct 18. PMID:17951245 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See Also DNA polymerase 3D structures

Proteopedia Page Contributors and Editors (what is this?)

OCA