2va3
From Proteopedia
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|PDB= 2va3 |SIZE=350|CAPTION= <scene name='initialview01'>2va3</scene>, resolution 2.98Å | |PDB= 2va3 |SIZE=350|CAPTION= <scene name='initialview01'>2va3</scene>, resolution 2.98Å | ||
|SITE= <scene name='pdbsite=AC1:Dgt+Binding+Site+For+Chain+A'>AC1</scene>, <scene name='pdbsite=AC2:Ca+Binding+Site+For+Chain+A'>AC2</scene>, <scene name='pdbsite=AC3:Ca+Binding+Site+For+Chain+A'>AC3</scene> and <scene name='pdbsite=AC4:Ca+Binding+Site+For+Chain+A'>AC4</scene> | |SITE= <scene name='pdbsite=AC1:Dgt+Binding+Site+For+Chain+A'>AC1</scene>, <scene name='pdbsite=AC2:Ca+Binding+Site+For+Chain+A'>AC2</scene>, <scene name='pdbsite=AC3:Ca+Binding+Site+For+Chain+A'>AC3</scene> and <scene name='pdbsite=AC4:Ca+Binding+Site+For+Chain+A'>AC4</scene> | ||
| - | |LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene> | + | |LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DA:2'-DEOXYADENOSINE-5'-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DFT:1-[2-DEOXYRIBOFURANOSYL]-2,4-DIFLUORO-5-METHYL-BENZENE-5'MONOPHOSPHATE'>DFT</scene>, <scene name='pdbligand=DG:2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DGT:2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE'>DGT</scene>, <scene name='pdbligand=DT:THYMIDINE-5'-MONOPHOSPHATE'>DT</scene> |
| - | |ACTIVITY= [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] | + | |ACTIVITY= <span class='plainlinks'>[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] </span> |
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[2asl|2ASL]], [[1s0m|1S0M]], [[2jeg|2JEG]], [[1rys|1RYS]], [[2j6t|2J6T]], [[1n56|1N56]], [[2atl|2ATL]], [[1jx4|1JX4]], [[2c22|2C22]], [[2va2|2VA2]], [[1s97|1S97]], [[2agq|2AGQ]], [[2jej|2JEJ]], [[2ago|2AGO]], [[2asj|2ASJ]], [[2asd|2ASD]], [[1n48|1N48]], [[1jxl|1JXL]], [[2bq3|2BQ3]], [[2uvu|2UVU]], [[2j6u|2J6U]], [[2agp|2AGP]], [[1s0n|1S0N]], [[2c2r|2C2R]], [[2jef|2JEF]], [[1s0o|1S0O]], [[2uvw|2UVW]], [[2bqr|2BQR]], [[2jei|2JEI]], [[1s9f|1S9F]], [[2au0|2AU0]], [[2bqu|2BQU]], [[2c28|2C28]], [[2v9w|2V9W]], [[2c2e|2C2E]], [[1ryr|1RYR]], [[2uvv|2UVV]], [[2c2d|2C2D]], [[2br0|2BR0]], [[1s10|1S10]], [[2j6s|2J6S]], [[2uvr|2UVR]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2va3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2va3 OCA], [http://www.ebi.ac.uk/pdbsum/2va3 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2va3 RCSB]</span> | ||
}} | }} | ||
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[[Category: Irimia, A.]] | [[Category: Irimia, A.]] | ||
[[Category: Pallan, P S.]] | [[Category: Pallan, P S.]] | ||
| - | [[Category: CA]] | ||
| - | [[Category: DGT]] | ||
[[Category: 2]] | [[Category: 2]] | ||
[[Category: 4-difluorotoluene]] | [[Category: 4-difluorotoluene]] | ||
| Line 45: | Line 46: | ||
[[Category: translesion dna polymerase]] | [[Category: translesion dna polymerase]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:10:11 2008'' |
Revision as of 02:10, 31 March 2008
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| , resolution 2.98Å | |||||||
|---|---|---|---|---|---|---|---|
| Sites: | , , and | ||||||
| Ligands: | , , , , , , | ||||||
| Activity: | DNA-directed DNA polymerase, with EC number 2.7.7.7 | ||||||
| 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
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| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
COMPLEX STRUCTURE OF SULFOLOBUS SOLFATARICUS DPO4 AND DNA DUPLEX CONTAINING A HYDROPHOBIC THYMINE ISOSTERE 2,4-DIFLUOROTOLUENE NUCLEOTIDE IN THE TEMPLATE STRAND
Overview
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 Structure
2VA3 is a Single protein structure of sequence from Sulfolobus solfataricus. Full crystallographic information is available from OCA.
Reference
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
Page seeded by OCA on Mon Mar 31 05:10:11 2008
Categories: DNA-directed DNA polymerase | Single protein | Sulfolobus solfataricus | Egli, M. | Irimia, A. | Pallan, P S. | 2 | 4-difluorotoluene | Cytoplasm | Dgtp | 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
