2agq
From Proteopedia
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|PDB= 2agq |SIZE=350|CAPTION= <scene name='initialview01'>2agq</scene>, resolution 2.10Å | |PDB= 2agq |SIZE=350|CAPTION= <scene name='initialview01'>2agq</scene>, resolution 2.10Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand= | + | |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=DG:2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DOC:2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE'>DOC</scene>, <scene name='pdbligand=DT:THYMIDINE-5'-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=DTP:2'-DEOXYADENOSINE+5'-TRIPHOSPHATE'>DTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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= dbh, dpo4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2287 Sulfolobus solfataricus]) | |GENE= dbh, dpo4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2287 Sulfolobus solfataricus]) | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[1jx4|1JX4]], [[1jxl|1JXL]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2agq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2agq OCA], [http://www.ebi.ac.uk/pdbsum/2agq PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2agq RCSB]</span> | ||
}} | }} | ||
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[[Category: Ling, H.]] | [[Category: Ling, H.]] | ||
[[Category: Yang, W.]] | [[Category: Yang, W.]] | ||
| - | [[Category: CA]] | ||
| - | [[Category: DTP]] | ||
| - | [[Category: MG]] | ||
[[Category: base stacking]] | [[Category: base stacking]] | ||
[[Category: fidelity]] | [[Category: fidelity]] | ||
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[[Category: pyrophosphorolysis]] | [[Category: pyrophosphorolysis]] | ||
| - | ''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 01:52:26 2008'' |
Revision as of 22:52, 30 March 2008
| |||||||
| , resolution 2.10Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , , , , , | ||||||
| Gene: | dbh, dpo4 (Sulfolobus solfataricus) | ||||||
| Activity: | DNA-directed DNA polymerase, with EC number 2.7.7.7 | ||||||
| Related: | 1JX4, 1JXL
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Fidelity of Dpo4: effect of metal ions, nucleotide selection and pyrophosphorolysis
Overview
We report the crystal structures of a translesion DNA polymerase, Dpo4, complexed with a matched or mismatched incoming nucleotide and with a pyrophosphate product after misincorporation. These structures suggest two mechanisms by which Dpo4 may reject a wrong incoming nucleotide with its preformed and open active site. First, a mismatched replicating base pair leads to poor base stacking and alignment of the metal ions and as a consequence, inhibits incorporation. By replacing Mg2+ with Mn2+, which has a relaxed coordination requirement and tolerates misalignment, the catalytic efficiency of misincorporation increases dramatically. Mn2+ also enhances translesion synthesis by Dpo4. Subtle conformational changes that lead to the proper metal ion coordination may, therefore, be a key step in catalysis. Second, the slow release of pyrophosphate may increase the fidelity of Dpo4 by stalling mispaired primer extension and promoting pyrophosphorolysis that reverses the polymerization reaction. Indeed, Dpo4 has robust pyrophosphorolysis activity and degrades the primer strand in the presence of pyrophosphate. The correct incoming nucleotide allows DNA synthesis to overcome pyrophosphorolysis, but an incorrect incoming nucleotide does not.
About this Structure
2AGQ is a Single protein structure of sequence from Sulfolobus solfataricus. Full crystallographic information is available from OCA.
Reference
Fidelity of Dpo4: effect of metal ions, nucleotide selection and pyrophosphorolysis., Vaisman A, Ling H, Woodgate R, Yang W, EMBO J. 2005 Sep 7;24(17):2957-67. Epub 2005 Aug 18. PMID:16107880
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