1d5a: Difference between revisions
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[[Image:1d5a.jpg|left|200px]] | [[Image:1d5a.jpg|left|200px]] | ||
'''CRYSTAL STRUCTURE OF AN ARCHAEBACTERIAL DNA POLYMERASE D.TOK. DEPOSITION OF SECOND NATIVE STRUCTURE AT 2.4 ANGSTROM''' | {{Structure | ||
|PDB= 1d5a |SIZE=350|CAPTION= <scene name='initialview01'>1d5a</scene>, resolution 2.4Å | |||
|SITE= | |||
|LIGAND= <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene> and <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] | |||
|GENE= | |||
}} | |||
'''CRYSTAL STRUCTURE OF AN ARCHAEBACTERIAL DNA POLYMERASE D.TOK. DEPOSITION OF SECOND NATIVE STRUCTURE AT 2.4 ANGSTROM''' | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
1D5A is a [ | 1D5A is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Desulfurococcus_sp._tok Desulfurococcus sp. tok]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D5A OCA]. | ||
==Reference== | ==Reference== | ||
Crystal structure of an archaebacterial DNA polymerase., Zhao Y, Jeruzalmi D, Moarefi I, Leighton L, Lasken R, Kuriyan J, Structure. 1999 Oct 15;7(10):1189-99. PMID:[http:// | Crystal structure of an archaebacterial DNA polymerase., Zhao Y, Jeruzalmi D, Moarefi I, Leighton L, Lasken R, Kuriyan J, Structure. 1999 Oct 15;7(10):1189-99. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10545321 10545321] | ||
[[Category: DNA-directed DNA polymerase]] | [[Category: DNA-directed DNA polymerase]] | ||
[[Category: Desulfurococcus sp. tok]] | [[Category: Desulfurococcus sp. tok]] | ||
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[[Category: thermostable]] | [[Category: thermostable]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 10:33:02 2008'' | ||
Revision as of 11:33, 20 March 2008
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| , resolution 2.4Å | |||||||
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| Ligands: | and | ||||||
| Activity: | DNA-directed DNA polymerase, with EC number 2.7.7.7 | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
CRYSTAL STRUCTURE OF AN ARCHAEBACTERIAL DNA POLYMERASE D.TOK. DEPOSITION OF SECOND NATIVE STRUCTURE AT 2.4 ANGSTROM
OverviewOverview
BACKGROUND: Members of the Pol II family of DNA polymerases are responsible for chromosomal replication in eukaryotes, and carry out highly processive DNA replication when attached to ring-shaped processivity clamps. The sequences of Pol II polymerases are distinct from those of members of the well-studied Pol I family of DNA polymerases. The DNA polymerase from the archaebacterium Desulfurococcus strain Tok (D. Tok Pol) is a member of the Pol II family that retains catalytic activity at elevated temperatures. RESULTS: The crystal structure of D. Tok Pol has been determined at 2.4 A resolution. The architecture of this Pol II type DNA polymerase resembles that of the DNA polymerase from the bacteriophage RB69, with which it shares less than approximately 20% sequence identity. As in RB69, the central catalytic region of the DNA polymerase is located within the 'palm' subdomain and is strikingly similar in structure to the corresponding regions of Pol I type DNA polymerases. The structural scaffold that surrounds the catalytic core in D. Tok Pol is unrelated in structure to that of Pol I type polymerases. The 3'-5' proofreading exonuclease domain of D. Tok Pol resembles the corresponding domains of RB69 Pol and Pol I type DNA polymerases. The exonuclease domain in D. Tok Pol is located in the same position relative to the polymerase domain as seen in RB69, and on the opposite side of the palm subdomain compared to its location in Pol I type polymerases. The N-terminal domain of D. Tok Pol has structural similarity to RNA-binding domains. Sequence alignments suggest that this domain is conserved in the eukaryotic DNA polymerases delta and epsilon. CONCLUSIONS: The structure of D. Tok Pol confirms that the modes of binding of the template and extrusion of newly synthesized duplex DNA are likely to be similar in both Pol II and Pol I type DNA polymerases. However, the mechanism by which the newly synthesized product transits in and out of the proofreading exonuclease domain has to be quite different. The discovery of a domain that seems to be an RNA-binding module raises the possibility that Pol II family members interact with RNA.
About this StructureAbout this Structure
1D5A is a Single protein structure of sequence from Desulfurococcus sp. tok. Full crystallographic information is available from OCA.
ReferenceReference
Crystal structure of an archaebacterial DNA polymerase., Zhao Y, Jeruzalmi D, Moarefi I, Leighton L, Lasken R, Kuriyan J, Structure. 1999 Oct 15;7(10):1189-99. PMID:10545321
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