2pyl

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==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)==
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<StructureSection load='2pyl' size='340' side='right' caption='[[2pyl]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
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<StructureSection load='2pyl' size='340' side='right'caption='[[2pyl]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[2pyl]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpph2 Bpph2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PYL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PYL FirstGlance]. <br>
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<table><tr><td colspan='2'>[[2pyl]] is a 3 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=2PYL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PYL FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TTP:THYMIDINE-5-TRIPHOSPHATE'>TTP</scene></td></tr>
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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]] 2.2&#8491;</td></tr>
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<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=2DA:2,3-DIDEOXYADENOSINE-5-MONOPHOSPHATE'>2DA</scene></td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2DA:2,3-DIDEOXYADENOSINE-5-MONOPHOSPHATE'>2DA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TTP:THYMIDINE-5-TRIPHOSPHATE'>TTP</scene></td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2py5|2py5]], [[2pyj|2pyj]], [[2pzs|2pzs]]</td></tr>
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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=2pyl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pyl OCA], [https://pdbe.org/2pyl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pyl RCSB], [https://www.ebi.ac.uk/pdbsum/2pyl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pyl ProSAT]</span></td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">2, gp2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10756 BPPH2])</td></tr>
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<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><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></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2pyl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pyl OCA], [http://pdbe.org/2pyl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2pyl RCSB], [http://www.ebi.ac.uk/pdbsum/2pyl PDBsum]</span></td></tr>
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</table>
</table>
== Function ==
== Function ==
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[[http://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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[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 ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
Check<jmol>
<jmolCheckbox>
<jmolCheckbox>
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<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/py/2pyl_consurf.spt"</scriptWhenChecked>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/py/2pyl_consurf.spt"</scriptWhenChecked>
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
<text>to colour the structure by Evolutionary Conservation</text>
<text>to colour the structure by Evolutionary Conservation</text>
</jmolCheckbox>
</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/chain_selection.php?pdb_ID=2ata ConSurf].
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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=2pyl ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
<div style="background-color:#fffaf0;">
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==See Also==
==See Also==
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*[[DNA polymerase|DNA polymerase]]
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*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Bpph2]]
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[[Category: Bacillus virus phi29]]
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[[Category: DNA-directed DNA polymerase]]
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[[Category: Large Structures]]
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[[Category: Berman, A J]]
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[[Category: Berman AJ]]
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[[Category: Blanco, L]]
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[[Category: Blanco L]]
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[[Category: Goodman, J L]]
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[[Category: Goodman JL]]
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[[Category: Kamtekar, S]]
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[[Category: Kamtekar S]]
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[[Category: Lazaro, J M]]
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[[Category: Lazaro JM]]
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[[Category: Salas, M]]
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[[Category: Salas M]]
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[[Category: Steitz, T A]]
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[[Category: Steitz TA]]
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[[Category: Vega, M de]]
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[[Category: De Vega M]]
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[[Category: Protein-dna complex]]
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[[Category: Replication]]
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[[Category: Transferase-dna complex]]
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Current revision

Phi29 DNA polymerase complexed with primer-template DNA and incoming nucleotide substrates (ternary complex)

PDB ID 2pyl

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Proteopedia Page Contributors and Editors (what is this?)

OCA

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