2va2: Difference between revisions
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==About this Structure== | ==About this Structure== | ||
2VA2 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 <scene name='pdbligand=CA:'>CA</scene> and <scene name='pdbligand=DCT:'>DCT</scene> 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] Known structural/functional Sites: <scene name='pdbsite=AC1:Ca Binding Site For Chain A'>AC1</scene>, <scene name='pdbsite=AC2:Ca Binding Site For Chain A'>AC2</scene>, <scene name='pdbsite=AC3:Dct Binding Site For Chain A'>AC3</scene>, <scene name='pdbsite=AC4:Ca Binding Site For Chain A'>AC4</scene>, <scene name='pdbsite=AC5:Ca Binding Site For Chain A'>AC5</scene>, <scene name='pdbsite=AC6:Ca Binding Site For Chain B'>AC6</scene>, <scene name='pdbsite=AC7:Ca Binding Site For Chain B'>AC7</scene> and <scene name='pdbsite=AC8:Dct Binding Site For Chain E'>AC8</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VA2 OCA]. | 2VA2 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 <scene name='pdbligand=CA:'>CA</scene> and <scene name='pdbligand=DCT:'>DCT</scene> 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] Known structural/functional Sites: <scene name='pdbsite=AC1:Ca+Binding+Site+For+Chain+A'>AC1</scene>, <scene name='pdbsite=AC2:Ca+Binding+Site+For+Chain+A'>AC2</scene>, <scene name='pdbsite=AC3:Dct+Binding+Site+For+Chain+A'>AC3</scene>, <scene name='pdbsite=AC4:Ca+Binding+Site+For+Chain+A'>AC4</scene>, <scene name='pdbsite=AC5:Ca+Binding+Site+For+Chain+A'>AC5</scene>, <scene name='pdbsite=AC6:Ca+Binding+Site+For+Chain+B'>AC6</scene>, <scene name='pdbsite=AC7:Ca+Binding+Site+For+Chain+B'>AC7</scene> and <scene name='pdbsite=AC8:Dct+Binding+Site+For+Chain+E'>AC8</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VA2 OCA]. | ||
==Reference== | ==Reference== | ||
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[[Category: translesion dna polymerase]] | [[Category: translesion dna polymerase]] | ||
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Revision as of 11:50, 3 February 2008
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COMPLEX STRUCTURE OF SULFOLOBUS SOLFATARICUS DPO4 AND DNA DUPLEX CONTAINING A HYDROPHOBIC THYMINE ISOSTERE 2,4-DIFLUOROTOLUENE NUCLEOTIDE IN THE TEMPLATE STRAND
OverviewOverview
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.
About this StructureAbout this Structure
2VA2 is a Single protein structure of sequence from Sulfolobus solfataricus with and as ligands. Active as DNA-directed DNA polymerase, with EC number 2.7.7.7 Known structural/functional Sites: , , , , , , and . Full crystallographic information is available from OCA.
ReferenceReference
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
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- DNA-directed DNA polymerase
- Single protein
- Sulfolobus solfataricus
- Egli, M.
- Irimia, A.
- Pallan, P.S.
- CA
- DCT
- 2
- 2-4-difluorotoluene
- Cytoplasm
- Ddctp
- Dna damage
- Dna repair
- Dna replication
- Dna-binding
- Dna-directed dna polymerase
- Magnesium
- Metal-binding
- Mutator protein
- Nucleotidyltransferase
- P2 dna polymerase iv
- Transferase
- Translesion dna polymerase