2c22: Difference between revisions
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|PDB= 2c22 |SIZE=350|CAPTION= <scene name='initialview01'>2c22</scene>, resolution 2.56Å | |PDB= 2c22 |SIZE=350|CAPTION= <scene name='initialview01'>2c22</scene>, resolution 2.56Å | ||
|SITE= <scene name='pdbsite=AC1:Ca+Binding+Site+For+Chain+A'>AC1</scene> | |SITE= <scene name='pdbsite=AC1:Ca+Binding+Site+For+Chain+A'>AC1</scene> | ||
|LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene> | |LIGAND= <scene name='pdbligand=8OG:8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE'>8OG</scene>, <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=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= | |||
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2c22 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c22 OCA], [http://www.ebi.ac.uk/pdbsum/2c22 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2c22 RCSB]</span> | |||
}} | }} | ||
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[[Category: Irimia, A.]] | [[Category: Irimia, A.]] | ||
[[Category: Loukachevitch, L V.]] | [[Category: Loukachevitch, L V.]] | ||
[[Category: 7,8-dihydro-8-oxodeoxyguanosine]] | |||
[[Category: 7 | |||
[[Category: dna damage]] | [[Category: dna damage]] | ||
[[Category: dna repair]] | [[Category: dna repair]] | ||
| Line 43: | Line 43: | ||
[[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 02:15:07 2008'' | ||
Revision as of 02:15, 31 March 2008
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| , resolution 2.56Å | |||||||
|---|---|---|---|---|---|---|---|
| Sites: | |||||||
| Ligands: | , , , , , , | ||||||
| Activity: | DNA-directed DNA polymerase, with EC number 2.7.7.7 | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
EFFICIENT AND HIGH FIDELITY INCORPORATION OF DCTP OPPOSITE 7,8-DIHYDRO-8-OXODEOXYGUANOSINE BY SULFOLOBUS SOLFATARICUS DNA POLYMERASE DPO4
OverviewOverview
DNA polymerases insert dATP opposite the oxidative damage product 7,8-dihydro-8-oxodeoxyguanosine (8-oxoG) instead of dCTP, to the extent of >90% with some polymerases. Steady-state kinetics with the Y-family Sulfolobus solfataricus DNA polymerase IV (Dpo4) showed 90-fold higher incorporation efficiency of dCTP > dATP opposite 8-oxoG and 4-fold higher efficiency of extension beyond an 8-oxoG:C pair than an 8-oxoG:A pair. The catalytic efficiency for these events (with dCTP or C) was similar for G and 8-oxoG templates. Mass spectral analysis of extended DNA primers showed >/=95% incorporation of dCTP > dATP opposite 8-oxoG. Pre-steady-state kinetics showed faster rates of dCTP incorporation opposite 8-oxoG than G. The measured K(d)(,dCTP) was 15-fold lower for an oligonucleotide containing 8-oxoG than with G. Extension beyond an 8-oxoG:C pair was similar to G:C and faster than for an 8-oxoG:A pair, in contrast to other polymerases. The E(a) for dCTP insertion opposite 8-oxoG was lower than for opposite G. Crystal structures of Dpo4 complexes with oligonucleotides were solved with C, A, and G nucleoside triphosphates placed opposite 8-oxoG. With ddCTP, dCTP, and dATP the phosphodiester bonds were formed even in the presence of Ca(2+). The 8-oxoG:C pair showed classic Watson-Crick geometry; the 8-oxoG:A pair was in the syn:anti configuration, with the A hybridized in a Hoogsteen pair with 8-oxoG. With dGTP placed opposite 8-oxoG, pairing was not to the 8-oxoG but to the 5' C (and in classic Watson-Crick geometry), consistent with the low frequency of this frameshift event observed in the catalytic assays.
About this StructureAbout this Structure
2C22 is a Single protein structure of sequence from Sulfolobus solfataricus. Full crystallographic information is available from OCA.
ReferenceReference
Efficient and high fidelity incorporation of dCTP opposite 7,8-dihydro-8-oxodeoxyguanosine by Sulfolobus solfataricus DNA polymerase Dpo4., Zang H, Irimia A, Choi JY, Angel KC, Loukachevitch LV, Egli M, Guengerich FP, J Biol Chem. 2006 Jan 27;281(4):2358-72. Epub 2005 Nov 22. PMID:16306039
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Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)
OCA- Pages with broken file links
- DNA-directed DNA polymerase
- Single protein
- Sulfolobus solfataricus
- Egli, M.
- Irimia, A.
- Loukachevitch, L V.
- 7,8-dihydro-8-oxodeoxyguanosine
- 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