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[[Image:1ig9.gif|left|200px]]
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{{STRUCTURE_1ig9|  PDB=1ig9  |  SCENE=  }}
'''Structure of the Replicating Complex of a Pol Alpha Family DNA Polymerase'''


==Structure of the Replicating Complex of a Pol Alpha Family DNA Polymerase==
<StructureSection load='1ig9' size='340' side='right'caption='[[1ig9]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1ig9]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_phage_RB69 Escherichia phage RB69]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IG9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IG9 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]] 2.6&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene>, <scene name='pdbligand=TTP:THYMIDINE-5-TRIPHOSPHATE'>TTP</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=1ig9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ig9 OCA], [https://pdbe.org/1ig9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ig9 RCSB], [https://www.ebi.ac.uk/pdbsum/1ig9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ig9 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/DPOL_BPR69 DPOL_BPR69] 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/ig/1ig9_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=1ig9 ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
We describe the 2.6 A resolution crystal structure of RB69 DNA polymerase with primer-template DNA and dTTP, capturing the step just before primer extension. This ternary complex structure in the human DNA polymerase alpha family shows a 60 degrees rotation of the fingers domain relative to the apo-protein structure, similar to the fingers movement in pol I family polymerases. Minor groove interactions near the primer 3' terminus suggest a common fidelity mechanism for pol I and pol alpha family polymerases. The duplex product DNA orientation differs by 40 degrees between the polymerizing mode and editing mode structures. The role of the thumb in this DNA motion provides a model for editing in the pol alpha family.


==Overview==
Structure of the replicating complex of a pol alpha family DNA polymerase.,Franklin MC, Wang J, Steitz TA Cell. 2001 Jun 1;105(5):657-67. PMID:11389835<ref>PMID:11389835</ref>
We describe the 2.6 A resolution crystal structure of RB69 DNA polymerase with primer-template DNA and dTTP, capturing the step just before primer extension. This ternary complex structure in the human DNA polymerase alpha family shows a 60 degrees rotation of the fingers domain relative to the apo-protein structure, similar to the fingers movement in pol I family polymerases. Minor groove interactions near the primer 3' terminus suggest a common fidelity mechanism for pol I and pol alpha family polymerases. The duplex product DNA orientation differs by 40 degrees between the polymerizing mode and editing mode structures. The role of the thumb in this DNA motion provides a model for editing in the pol alpha family.


==About this Structure==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
1IG9 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_rb69 Enterobacteria phage rb69]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IG9 OCA].
</div>
<div class="pdbe-citations 1ig9" style="background-color:#fffaf0;"></div>


==Reference==
==See Also==
Structure of the replicating complex of a pol alpha family DNA polymerase., Franklin MC, Wang J, Steitz TA, Cell. 2001 Jun 1;105(5):657-67. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11389835 11389835]
*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
[[Category: DNA-directed DNA polymerase]]
== References ==
[[Category: Enterobacteria phage rb69]]
<references/>
[[Category: Single protein]]
__TOC__
[[Category: Franklin, M C.]]
</StructureSection>
[[Category: Steitz, T A.]]
[[Category: Escherichia phage RB69]]
[[Category: Wang, J.]]
[[Category: Large Structures]]
[[Category: Catalytic complex]]
[[Category: Franklin MC]]
[[Category: Dna polymerase]]
[[Category: Steitz TA]]
[[Category: Fidelity]]
[[Category: Wang J]]
[[Category: Two metal ion mechanism]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May  2 19:58:08 2008''

Latest revision as of 08:33, 16 August 2023

Structure of the Replicating Complex of a Pol Alpha Family DNA Polymerase

1ig9, resolution 2.60Å

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