2dtu
From Proteopedia
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|PDB= 2dtu |SIZE=350|CAPTION= <scene name='initialview01'>2dtu</scene>, resolution 2.370Å | |PDB= 2dtu |SIZE=350|CAPTION= <scene name='initialview01'>2dtu</scene>, resolution 2.370Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= | + | |LIGAND= <scene name='pdbligand=3DR:1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE'>3DR</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=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= 43 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id= | + | |GENE= 43 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=12353 Enterobacteria phage RB69]) |
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[1clq|1CLQ]], [[1ig9|1IG9]], [[1rv2|1RV2]], [[1q9x|1Q9X]], [[1q9y|1Q9Y]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2dtu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dtu OCA], [http://www.ebi.ac.uk/pdbsum/2dtu PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2dtu RCSB]</span> | ||
}} | }} | ||
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==About this Structure== | ==About this Structure== | ||
| - | 2DTU is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/ | + | 2DTU is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_rb69 Enterobacteria phage rb69]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DTU OCA]. |
==Reference== | ==Reference== | ||
Structural and biochemical investigation of the role in proofreading of a beta hairpin loop found in the exonuclease domain of a replicative DNA polymerase of the B family., Hogg M, Aller P, Konigsberg W, Wallace SS, Doublie S, J Biol Chem. 2007 Jan 12;282(2):1432-44. Epub 2006 Nov 9. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17098747 17098747] | Structural and biochemical investigation of the role in proofreading of a beta hairpin loop found in the exonuclease domain of a replicative DNA polymerase of the B family., Hogg M, Aller P, Konigsberg W, Wallace SS, Doublie S, J Biol Chem. 2007 Jan 12;282(2):1432-44. Epub 2006 Nov 9. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17098747 17098747] | ||
[[Category: DNA-directed DNA polymerase]] | [[Category: DNA-directed DNA polymerase]] | ||
| - | [[Category: Enterobacteria phage | + | [[Category: Enterobacteria phage rb69]] |
[[Category: Single protein]] | [[Category: Single protein]] | ||
[[Category: Aller, P.]] | [[Category: Aller, P.]] | ||
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[[Category: dna polymerase]] | [[Category: 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 02:39:25 2008'' |
Revision as of 23:39, 30 March 2008
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| , resolution 2.370Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , , | ||||||
| Gene: | 43 (Enterobacteria phage RB69) | ||||||
| Activity: | DNA-directed DNA polymerase, with EC number 2.7.7.7 | ||||||
| Related: | 1CLQ, 1IG9, 1RV2, 1Q9X, 1Q9Y
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal structure of the beta hairpin loop deletion variant of RB69 gp43 in complex with DNA containing an abasic site analog
Overview
Replicative DNA polymerases, as exemplified by the B family polymerases from bacteriophages T4 and RB69, not only replicate DNA but also have the ability to proofread misincorporated nucleotides. Because the two activities reside in separate protein domains, polymerases must employ a mechanism that allows for efficient switching of the primer strand between the two active sites to achieve fast and accurate replication. Prior mutational and structural studies suggested that a beta hairpin structure located in the exonuclease domain of family B polymerases might play an important role in active site switching in the event of a nucleotide misincorporation. We show that deleting the beta hairpin loop in RB69 gp43 affects neither polymerase nor exonuclease activities. Single binding event studies with mismatched primer termini, however, show that the beta hairpin plays a role in maintaining the stability of the polymerase/DNA interactions during the binding of the primer DNA in the exonuclease active site but not on the return of the corrected primer to the polymerase active site. In addition, the deletion variant showed a more stable incorporation of a nucleotide opposite an abasic site. Moreover, in the 2.4 A crystal structure of the beta hairpin deletion variant incorporating an A opposite a templating furan, all four molecules in the crystal asymmetric unit have DNA in the polymerase active site, despite the presence of DNA distortions because of the misincorporation, confirming that the primer strand is not stably bound within the exonuclease active site in the absence of the beta hairpin loop.
About this Structure
2DTU is a Single protein structure of sequence from Enterobacteria phage rb69. Full crystallographic information is available from OCA.
Reference
Structural and biochemical investigation of the role in proofreading of a beta hairpin loop found in the exonuclease domain of a replicative DNA polymerase of the B family., Hogg M, Aller P, Konigsberg W, Wallace SS, Doublie S, J Biol Chem. 2007 Jan 12;282(2):1432-44. Epub 2006 Nov 9. PMID:17098747
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