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[[Image:2pyj.gif|left|200px]]
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{{STRUCTURE_2pyj|  PDB=2pyj  |  SCENE=  }}
'''Phi29 DNA polymerase complexed with primer-template DNA and incoming nucleotide substrates (ternary complex)'''


==Phi29 DNA polymerase complexed with primer-template DNA and incoming nucleotide substrates (ternary complex)==
<StructureSection load='2pyj' size='340' side='right'caption='[[2pyj]], [[Resolution|resolution]] 2.03&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2pyj]] is a 8 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=2PYJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PYJ FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.03&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DGT:2-DEOXYGUANOSINE-5-TRIPHOSPHATE'>DGT</scene>, <scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2pyj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pyj OCA], [https://pdbe.org/2pyj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pyj RCSB], [https://www.ebi.ac.uk/pdbsum/2pyj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pyj ProSAT]</span></td></tr>
</table>
== Function ==
[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.
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/py/2pyj_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</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=2pyj ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Replicative DNA polymerases (DNAPs) move along template DNA in a processive manner. The structural basis of the mechanism of translocation has been better studied in the A-family of polymerases than in the B-family of replicative polymerases. To address this issue, we have determined the X-ray crystal structures of phi29 DNAP, a member of the protein-primed subgroup of the B-family of polymerases, complexed with primer-template DNA in the presence or absence of the incoming nucleoside triphosphate, the pre- and post-translocated states, respectively. Comparison of these structures reveals a mechanism of translocation that appears to be facilitated by the coordinated movement of two conserved tyrosine residues into the insertion site. This differs from the mechanism employed by the A-family polymerases, in which a conserved tyrosine moves into the templating and insertion sites during the translocation step. Polymerases from the two families also interact with downstream single-stranded template DNA in very different ways.


==Overview==
Structures of phi29 DNA polymerase complexed with substrate: the mechanism of translocation in B-family polymerases.,Berman AJ, Kamtekar S, Goodman JL, Lazaro JM, de Vega M, Blanco L, Salas M, Steitz TA EMBO J. 2007 Jul 25;26(14):3494-505. Epub 2007 Jul 5. PMID:17611604<ref>PMID:17611604</ref>
Replicative DNA polymerases (DNAPs) move along template DNA in a processive manner. The structural basis of the mechanism of translocation has been better studied in the A-family of polymerases than in the B-family of replicative polymerases. To address this issue, we have determined the X-ray crystal structures of phi29 DNAP, a member of the protein-primed subgroup of the B-family of polymerases, complexed with primer-template DNA in the presence or absence of the incoming nucleoside triphosphate, the pre- and post-translocated states, respectively. Comparison of these structures reveals a mechanism of translocation that appears to be facilitated by the coordinated movement of two conserved tyrosine residues into the insertion site. This differs from the mechanism employed by the A-family polymerases, in which a conserved tyrosine moves into the templating and insertion sites during the translocation step. Polymerases from the two families also interact with downstream single-stranded template DNA in very different ways.


==About this Structure==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
2PYJ is a [[Single protein]] structure of sequence 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=2PYJ OCA].
</div>
<div class="pdbe-citations 2pyj" style="background-color:#fffaf0;"></div>


==Reference==
==See Also==
Structures of phi29 DNA polymerase complexed with substrate: the mechanism of translocation in B-family polymerases., Berman AJ, Kamtekar S, Goodman JL, Lazaro JM, de Vega M, Blanco L, Salas M, Steitz TA, EMBO J. 2007 Jul 25;26(14):3494-505. Epub 2007 Jul 5. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17611604 17611604]
*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
[[Category: Bacillus phage phi29]]
== References ==
[[Category: DNA-directed DNA polymerase]]
<references/>
[[Category: Single protein]]
__TOC__
[[Category: Berman, A J.]]
</StructureSection>
[[Category: Blanco, L.]]
[[Category: Bacillus virus phi29]]
[[Category: Goodman, J L.]]
[[Category: Large Structures]]
[[Category: Kamtekar, S.]]
[[Category: Berman AJ]]
[[Category: Lazaro, J M.]]
[[Category: Blanco L]]
[[Category: Salas, M.]]
[[Category: Goodman JL]]
[[Category: Steitz, T A.]]
[[Category: Kamtekar S]]
[[Category: Vega, M de.]]
[[Category: Lazaro JM]]
[[Category: Protein-dna complex]]
[[Category: Salas M]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 14:01:15 2008''
[[Category: Steitz TA]]
[[Category: De Vega M]]
Retrieved from "https://proteopedia.org/2pyj"