2ex3: Difference between revisions
New page: left|200px<br /><applet load="2ex3" size="450" color="white" frame="true" align="right" spinBox="true" caption="2ex3, resolution 3.000Å" /> '''Bacteriophage phi29... |
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[[Image:2ex3.gif|left|200px]]<br /><applet load="2ex3" size=" | [[Image:2ex3.gif|left|200px]]<br /><applet load="2ex3" size="350" color="white" frame="true" align="right" spinBox="true" | ||
caption="2ex3, resolution 3.000Å" /> | caption="2ex3, resolution 3.000Å" /> | ||
'''Bacteriophage phi29 DNA polymerase bound to terminal protein'''<br /> | '''Bacteriophage phi29 DNA polymerase bound to terminal protein'''<br /> | ||
==Overview== | ==Overview== | ||
The absolute requirement for primers in the initiation of DNA synthesis | The absolute requirement for primers in the initiation of DNA synthesis poses a problem for replicating the ends of linear chromosomes. The DNA polymerase of bacteriophage phi29 solves this problem by using a serine hydroxyl of terminal protein to prime replication. The 3.0 A resolution structure shows one domain of terminal protein making no interactions, a second binding the polymerase and a third domain containing the priming serine occupying the same binding cleft in the polymerase as duplex DNA does during elongation. Thus, the progressively elongating DNA duplex product must displace this priming domain. Further, this heterodimer of polymerase and terminal protein cannot accommodate upstream template DNA, thereby explaining its specificity for initiating DNA synthesis only at the ends of the bacteriophage genome. We propose a model for the transition from the initiation to the elongation phases in which the priming domain of terminal protein moves out of the active site as polymerase elongates the primer strand. The model indicates that terminal protein should dissociate from polymerase after the incorporation of approximately six nucleotides. | ||
==About this Structure== | ==About this Structure== | ||
2EX3 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Vibrio_phage_f237 Vibrio phage f237] with PB as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [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] Full crystallographic information is available from [http:// | 2EX3 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Vibrio_phage_f237 Vibrio phage f237] with <scene name='pdbligand=PB:'>PB</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [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] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EX3 OCA]. | ||
==Reference== | ==Reference== | ||
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[[Category: Protein complex]] | [[Category: Protein complex]] | ||
[[Category: Vibrio phage f237]] | [[Category: Vibrio phage f237]] | ||
[[Category: Berman, A | [[Category: Berman, A J.]] | ||
[[Category: Blanco, L.]] | [[Category: Blanco, L.]] | ||
[[Category: Kamtekar, S.]] | [[Category: Kamtekar, S.]] | ||
[[Category: Salas, M.]] | [[Category: Salas, M.]] | ||
[[Category: Steitz, T | [[Category: Steitz, T A.]] | ||
[[Category: Vega, M | [[Category: Vega, M de.]] | ||
[[Category: Wang, J.]] | [[Category: Wang, J.]] | ||
[[Category: PB]] | [[Category: PB]] | ||
[[Category: dna polymerase: protein primer complex]] | [[Category: dna polymerase: protein primer complex]] | ||
''Page seeded by [http:// | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 17:15:28 2008'' | ||
Revision as of 18:15, 21 February 2008
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Bacteriophage phi29 DNA polymerase bound to terminal protein
OverviewOverview
The absolute requirement for primers in the initiation of DNA synthesis poses a problem for replicating the ends of linear chromosomes. The DNA polymerase of bacteriophage phi29 solves this problem by using a serine hydroxyl of terminal protein to prime replication. The 3.0 A resolution structure shows one domain of terminal protein making no interactions, a second binding the polymerase and a third domain containing the priming serine occupying the same binding cleft in the polymerase as duplex DNA does during elongation. Thus, the progressively elongating DNA duplex product must displace this priming domain. Further, this heterodimer of polymerase and terminal protein cannot accommodate upstream template DNA, thereby explaining its specificity for initiating DNA synthesis only at the ends of the bacteriophage genome. We propose a model for the transition from the initiation to the elongation phases in which the priming domain of terminal protein moves out of the active site as polymerase elongates the primer strand. The model indicates that terminal protein should dissociate from polymerase after the incorporation of approximately six nucleotides.
About this StructureAbout this Structure
2EX3 is a Protein complex structure of sequences from Vibrio phage f237 with as ligand. Active as DNA-directed DNA polymerase, with EC number 2.7.7.7 Full crystallographic information is available from OCA.
ReferenceReference
The phi29 DNA polymerase:protein-primer structure suggests a model for the initiation to elongation transition., Kamtekar S, Berman AJ, Wang J, Lazaro JM, de Vega M, Blanco L, Salas M, Steitz TA, EMBO J. 2006 Mar 22;25(6):1335-43. Epub 2006 Mar 2. PMID:16511564
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