2ex3

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[[Image:2ex3.gif|left|200px]]
 
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{{Structure
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==Bacteriophage phi29 DNA polymerase bound to terminal protein==
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|PDB= 2ex3 |SIZE=350|CAPTION= <scene name='initialview01'>2ex3</scene>, resolution 3.000&Aring;
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<StructureSection load='2ex3' size='340' side='right'caption='[[2ex3]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=PB:LEAD+(II)+ION'>PB</scene>, <scene name='pdbligand=UNK:UNKNOWN'>UNK</scene>
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<table><tr><td colspan='2'>[[2ex3]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_virus_phi29 Bacillus virus phi29]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EX3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2EX3 FirstGlance]. <br>
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|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>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3&#8491;</td></tr>
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|GENE= 2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10756 Bacillus phage phi29]), 3 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10756 Bacillus phage phi29])
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PB:LEAD+(II)+ION'>PB</scene></td></tr>
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|DOMAIN=
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2ex3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ex3 OCA], [https://pdbe.org/2ex3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ex3 RCSB], [https://www.ebi.ac.uk/pdbsum/2ex3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ex3 ProSAT]</span></td></tr>
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|RELATEDENTRY=[[1xhx|1XHX]], [[1xhz|1XHZ]], [[1xi1|1XI1]]
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ex3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ex3 OCA], [http://www.ebi.ac.uk/pdbsum/2ex3 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2ex3 RCSB]</span>
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== Function ==
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}}
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[https://www.uniprot.org/uniprot/DPOL_BPPH2 DPOL_BPPH2] This polymerase possesses two enzymatic activities: DNA synthesis (polymerase) and an exonucleolytic activity that degrades single-stranded DNA in the 3'- to 5'-direction.
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ex/2ex3_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2ex3 ConSurf].
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<div style="clear:both"></div>
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'''Bacteriophage phi29 DNA polymerase bound to terminal protein'''
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==See Also==
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*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
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__TOC__
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==Overview==
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</StructureSection>
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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.
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[[Category: Bacillus virus phi29]]
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[[Category: Large Structures]]
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==About this Structure==
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[[Category: Berman AJ]]
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2EX3 is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Bacillus_phage_phi29 Bacillus phage phi29]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EX3 OCA].
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[[Category: Blanco L]]
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[[Category: Kamtekar S]]
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==Reference==
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[[Category: Salas M]]
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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:[http://www.ncbi.nlm.nih.gov/pubmed/16511564 16511564]
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[[Category: Steitz TA]]
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[[Category: Bacillus phage phi29]]
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[[Category: Wang J]]
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[[Category: DNA-directed DNA polymerase]]
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[[Category: De Vega M]]
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[[Category: Protein complex]]
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[[Category: Berman, A J.]]
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[[Category: Blanco, L.]]
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[[Category: Kamtekar, S.]]
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[[Category: Salas, M.]]
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[[Category: Steitz, T A.]]
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[[Category: Vega, M de.]]
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[[Category: Wang, J.]]
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[[Category: dna polymerase: protein primer complex]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 02:54:56 2008''
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Current revision

Bacteriophage phi29 DNA polymerase bound to terminal protein

PDB ID 2ex3

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