1xi1

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[[Image:1xi1.gif|left|200px]]
 
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{{Structure
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==Phi29 DNA polymerase ssDNA complex, monoclinic crystal form==
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|PDB= 1xi1 |SIZE=350|CAPTION= <scene name='initialview01'>1xi1</scene>, resolution 2.20&Aring;
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<StructureSection load='1xi1' size='340' side='right'caption='[[1xi1]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=DT:THYMIDINE-5&#39;-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>
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<table><tr><td colspan='2'>[[1xi1]] is a 4 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=1XI1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XI1 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]] 2.2&#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])
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=1xi1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xi1 OCA], [https://pdbe.org/1xi1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xi1 RCSB], [https://www.ebi.ac.uk/pdbsum/1xi1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xi1 ProSAT]</span></td></tr>
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|RELATEDENTRY=[[1xhx|1XHX]], [[1xhz|1XHZ]]
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1xi1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xi1 OCA], [http://www.ebi.ac.uk/pdbsum/1xi1 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1xi1 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/xi/1xi1_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=1xi1 ConSurf].
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<div style="clear:both"></div>
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'''Phi29 DNA polymerase ssDNA complex, monoclinic crystal form'''
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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 DNA polymerase from phage phi29 is a B family polymerase that initiates replication using a protein as a primer, attaching the first nucleotide of the phage genome to the hydroxyl of a specific serine of the priming protein. The crystal structure of phi29 DNA polymerase determined at 2.2 A resolution provides explanations for its extraordinary processivity and strand displacement activities. Homology modeling suggests that downstream template DNA passes through a tunnel prior to entering the polymerase active site. This tunnel is too small to accommodate double-stranded DNA and requires the separation of template and nontemplate strands. Members of the B family of DNA polymerases that use protein primers contain two sequence insertions: one forms a domain not previously observed in polymerases, while the second resembles the specificity loop of T7 RNA polymerase. The high processivity of phi29 DNA polymerase may be explained by its topological encirclement of both the downstream template and the upstream duplex DNA.
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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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1XI1 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=1XI1 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: Lazaro JM]]
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Insights into strand displacement and processivity from the crystal structure of the protein-primed DNA polymerase of bacteriophage phi29., Kamtekar S, Berman AJ, Wang J, Lazaro JM, de Vega M, Blanco L, Salas M, Steitz TA, Mol Cell. 2004 Nov 19;16(4):609-18. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15546620 15546620]
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[[Category: Salas M]]
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[[Category: Bacillus phage phi29]]
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[[Category: Steitz TA]]
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[[Category: DNA-directed DNA polymerase]]
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[[Category: Wang J]]
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[[Category: Single protein]]
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[[Category: De Vega M]]
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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: Lazaro, J M.]]
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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]]
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[[Category: processivity]]
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[[Category: protein-primed]]
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[[Category: replication]]
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[[Category: strand displacement]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 00:49:52 2008''
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Current revision

Phi29 DNA polymerase ssDNA complex, monoclinic crystal form

PDB ID 1xi1

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