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[[Image:1sl2.png|left|200px]]


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==Ternary 5' complex of T7 DNA polymerase with a DNA primer/template containing a cis-syn thymine dimer on the template and an incoming nucleotide==
The line below this paragraph, containing "STRUCTURE_1sl2", creates the "Structure Box" on the page.
<StructureSection load='1sl2' size='340' side='right'caption='[[1sl2]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)  
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[1sl2]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] and [https://en.wikipedia.org/wiki/Escherichia_phage_T7 Escherichia phage T7]. The July 2007 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Thymine Dimers''  by David S. Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2007_7 10.2210/rcsb_pdb/mom_2007_7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SL2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SL2 FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3&#8491;</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=DAD:2,3-DIDEOXYADENOSINE-5-TRIPHOSPHATE'>DAD</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TTD:CIS-SYN+CYCLOBUTANE+THYMINE+DIMER'>TTD</scene></td></tr>
{{STRUCTURE_1sl2| PDB=1sl2 |  SCENE= }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1sl2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sl2 OCA], [https://pdbe.org/1sl2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1sl2 RCSB], [https://www.ebi.ac.uk/pdbsum/1sl2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1sl2 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/DPOL_BPT7 DPOL_BPT7] Replicates viral genomic DNA. Non-processive DNA polymerase that achieves processivity by binding to host thioredoxin (TrxA). This interaction increases the rate of dNTP incorporation to yield a processivity of approximately 800 nucleotides (nt) per binding event. Interacts with DNA helicase gp4 to coordinate nucleotide polymerization with unwinding of the DNA. The leading strand is synthesized continuously while synthesis of the lagging strand requires the synthesis of oligoribonucleotides by the primase domain of gp4.<ref>PMID:9218486</ref> <ref>PMID:21606333</ref>
== 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/sl/1sl2_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=1sl2 ConSurf].
<div style="clear:both"></div>


'''Ternary 5' complex of T7 DNA polymerase with a DNA primer/template containing a cis-syn thymine dimer on the template and an incoming nucleotide'''
==See Also==
 
*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
 
*[[Thioredoxin 3D structures|Thioredoxin 3D structures]]
{{ABSTRACT_15235589}}
== References ==
 
<references/>
==About this Structure==
__TOC__
1SL2 is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t7 Enterobacteria phage t7] and [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. The following page contains interesting information on the relation of 1SL2 with [[http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb91_1.html Thymine Dimers]]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SL2 OCA].
</StructureSection>
[[Category: DNA-directed DNA polymerase]]
[[Category: Enterobacteria phage t7]]
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
[[Category: Protein complex]]
[[Category: Escherichia phage T7]]
[[Category: Large Structures]]
[[Category: RCSB PDB Molecule of the Month]]
[[Category: Thymine Dimers]]
[[Category: Thymine Dimers]]
[[Category: Bdour, H M.]]
[[Category: Bdour HM]]
[[Category: Doublie, S.]]
[[Category: Doublie S]]
[[Category: Dutta, S.]]
[[Category: Dutta S]]
[[Category: Ellenberger, T.]]
[[Category: Ellenberger T]]
[[Category: Li, Y.]]
[[Category: Li Y]]
[[Category: Taylor, J S.]]
[[Category: Taylor JS]]
[[Category: Close]]
[[Category: Dna polymerase]]
[[Category: Fidelity]]
[[Category: Lesion bypass]]
[[Category: Open]]
[[Category: Thymine dimer]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Jun 26 17:57:47 2008''

Latest revision as of 11:31, 14 February 2024

Ternary 5' complex of T7 DNA polymerase with a DNA primer/template containing a cis-syn thymine dimer on the template and an incoming nucleotideTernary 5' complex of T7 DNA polymerase with a DNA primer/template containing a cis-syn thymine dimer on the template and an incoming nucleotide

Structural highlights

1sl2 is a 4 chain structure with sequence from Escherichia coli and Escherichia phage T7. The July 2007 RCSB PDB Molecule of the Month feature on Thymine Dimers by David S. Goodsell is 10.2210/rcsb_pdb/mom_2007_7. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.3Å
Ligands:, , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

DPOL_BPT7 Replicates viral genomic DNA. Non-processive DNA polymerase that achieves processivity by binding to host thioredoxin (TrxA). This interaction increases the rate of dNTP incorporation to yield a processivity of approximately 800 nucleotides (nt) per binding event. Interacts with DNA helicase gp4 to coordinate nucleotide polymerization with unwinding of the DNA. The leading strand is synthesized continuously while synthesis of the lagging strand requires the synthesis of oligoribonucleotides by the primase domain of gp4.[1] [2]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

References

  1. ↑ Notarnicola SM, Mulcahy HL, Lee J, Richardson CC. The acidic carboxyl terminus of the bacteriophage T7 gene 4 helicase/primase interacts with T7 DNA polymerase. J Biol Chem. 1997 Jul 18;272(29):18425-33. PMID:9218486
  2. ↑ Zhang H, Lee SJ, Zhu B, Tran NQ, Tabor S, Richardson CC. Helicase-DNA polymerase interaction is critical to initiate leading-strand DNA synthesis. Proc Natl Acad Sci U S A. 2011 Jun 7;108(23):9372-7. doi:, 10.1073/pnas.1106678108. Epub 2011 May 23. PMID:21606333 doi:http://dx.doi.org/10.1073/pnas.1106678108

1sl2, resolution 2.30Å

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