First time at Proteopedia? Click on the green links: they change the 3D image. Click and drag the molecules. Proteopedia is a 3D, interactive encyclopedia of proteins, RNA, DNA and other molecules. With a free user account, you can edit pages in Proteopedia. Visit the Main Page to learn more.

2jef

From Proteopedia

Jump to: navigation, search


2jef, resolution 2.17Å ()
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, 2j6s, 2j6t, 2j6u, 2jeg, 2jei, 2jej
Resources: FirstGlance, OCA, RCSB, PDBsum
Coordinates: save as pdb, mmCIF, xml



Contents

The Molecular Basis of Selectivity of Nucleotide Triphosphate Incorporation Opposite O6-Benzylguanine by Sulfolobus solfataricus DNA Polymerase IV: Steady-state and Pre-steady-state and X-Ray Crystallography of Correct and Incorrect Pairing

Publication Abstract from PubMed

Previous work has shown that Sulfolobus solfataricus DNA polymerase Dpo4-catalyzed bypass of O(6)-methylguanine (O(6)-MeG) proceeds largely in an accurate but inefficient manner with a "wobble" base pairing between C and O(6)-MeG (Eoff, R. L., Irimia, A., Egli, M., and Guengerich, F. P. (2007) J. Biol. Chem. 282, 1456-1467). We considered here the bulky lesion O(6)-benzylguanine (O(6)-BzG) in DNA and catalysis by Dpo4. Mass spectrometry analysis of polymerization products revealed that the enzyme bypasses and extends across from O(6)-BzG, with C the major product ( approximately 70%) and some T and A ( approximately 15% each) incorporated opposite the lesion. Steady-state kinetic parameters indicated that Dpo4 was 7-, 5-, and 27-fold more efficient at C incorporation opposite O(6)-BzG than T, A, or G, respectively. In transient state kinetic analysis, the catalytic efficiency was decreased 62-fold for C incorporation opposite O(6)-BzG relative to unmodified DNA. Crystal structures reveal wobble pairing between C and O(6)-BzG. Pseudo-"Watson-Crick" pairing was observed between T and O(6)-BzG. Two other structures illustrate a possible mechanism for the accommodation of a +1 frameshift in the Dpo4 active site. The overall effect of O(6)-BzG is to decrease the efficiency of bypass by roughly an order of magnitude in every case except correct bypass, where the effect is not as pronounced. By comparison, Dpo4 is more accurate but no more efficient than model replicative polymerases, such as bacteriophage T7(-) DNA polymerase and human immunodeficiency virus-1 reverse transcriptase in the polymerization past O(6)-MeG and O(6)-BzG.

Molecular basis of selectivity of nucleoside triphosphate incorporation opposite O6-benzylguanine by sulfolobus solfataricus DNA polymerase Dpo4: steady-state and pre-steady-state kinetics and x-ray crystallography of correct and incorrect pairing., Eoff RL, Angel KC, Egli M, Guengerich FP, J Biol Chem. 2007 May 4;282(18):13573-84. Epub 2007 Mar 3. PMID:17337730

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

About this Structure

2jef is a 3 chain structure with sequence from Sulfolobus solfataricus p2. Full crystallographic information is available from OCA.

See Also

Reference

  • Eoff RL, Angel KC, Egli M, Guengerich FP. Molecular basis of selectivity of nucleoside triphosphate incorporation opposite O6-benzylguanine by sulfolobus solfataricus DNA polymerase Dpo4: steady-state and pre-steady-state kinetics and x-ray crystallography of correct and incorrect pairing. J Biol Chem. 2007 May 4;282(18):13573-84. Epub 2007 Mar 3. PMID:17337730 doi:10.1074/jbc.M700656200

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://www.proteopedia.org/wiki/index.php/2jef"
Personal tools