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[[Image:2py5.jpg|left|200px]]<br /><applet load="2py5" size="350" color="white" frame="true" align="right" spinBox="true"
caption="2py5, resolution 1.60&Aring;" />
'''Phi29 DNA polymerase complexed with single-stranded DNA'''<br />


==Overview==
==Phi29 DNA polymerase complexed with single-stranded DNA==
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.
<StructureSection load='2py5' size='340' side='right'caption='[[2py5]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2py5]] is a 7 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=2PY5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PY5 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]] 1.6&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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=2py5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2py5 OCA], [https://pdbe.org/2py5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2py5 RCSB], [https://www.ebi.ac.uk/pdbsum/2py5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2py5 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/2py5_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=2py5 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.


==About this Structure==
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>
2PY5 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Vibrio_phage_f237 Vibrio phage f237] with <scene name='pdbligand=EDO:'>EDO</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=2PY5 OCA].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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 5;. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17611604 17611604]
</div>
[[Category: DNA-directed DNA polymerase]]
<div class="pdbe-citations 2py5" style="background-color:#fffaf0;"></div>
[[Category: Single protein]]
[[Category: Vibrio phage f237]]
[[Category: Berman, A.J.]]
[[Category: Blanco, L.]]
[[Category: Goodman, J.L.]]
[[Category: Kamtekar, S.]]
[[Category: Lazaro, J.M.]]
[[Category: Salas, M.]]
[[Category: Steitz, T.A.]]
[[Category: Vega, M.de.]]
[[Category: EDO]]
[[Category: protein-dna complex]]


''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 23 14:14:46 2008''
==See Also==
*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Bacillus virus phi29]]
[[Category: Large Structures]]
[[Category: Berman AJ]]
[[Category: Blanco L]]
[[Category: Goodman JL]]
[[Category: Kamtekar S]]
[[Category: Lazaro JM]]
[[Category: Salas M]]
[[Category: Steitz TA]]
[[Category: De Vega M]]

Latest revision as of 11:12, 30 August 2023

Phi29 DNA polymerase complexed with single-stranded DNA

2py5, resolution 1.60Å

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