1x9s: Difference between revisions

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[[Image:1x9s.png|left|200px]]


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==T7 DNA polymerase in complex with a primer/template DNA containing a disordered N-2 aminofluorene on the template, crystallized with dideoxy-CTP as the incoming nucleotide.==
The line below this paragraph, containing "STRUCTURE_1x9s", creates the "Structure Box" on the page.
<StructureSection load='1x9s' size='340' side='right'caption='[[1x9s]], [[Resolution|resolution]] 2.70&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'>[[1x9s]] 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]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1X9S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1X9S 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]] 2.7&#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=2DT:3-DEOXYTHYMIDINE-5-MONOPHOSPHATE'>2DT</scene>, <scene name='pdbligand=AFG:N-(5-PHOSPHO-2-DEOXYGUANOSIN-8-YL)-2-AMINOFLUORENE'>AFG</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
{{STRUCTURE_1x9s|  PDB=1x9s  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1x9s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1x9s OCA], [https://pdbe.org/1x9s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1x9s RCSB], [https://www.ebi.ac.uk/pdbsum/1x9s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1x9s ProSAT]</span></td></tr>
 
</table>
===T7 DNA polymerase in complex with a primer/template DNA containing a disordered N-2 aminofluorene on the template, crystallized with dideoxy-CTP as the incoming nucleotide.===
== 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 ==
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    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/x9/1x9s_consurf.spt"</scriptWhenChecked>
{{ABSTRACT_PUBMED_15528277}}
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    <text>to colour the structure by Evolutionary Conservation</text>
==About this Structure==
  </jmolCheckbox>
[[1x9s]] is a 4 chain structure of [[Thioredoxin]] with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t7 Enterobacteria phage t7] and [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1X9S OCA].  
</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=1x9s ConSurf].
<div style="clear:both"></div>


==See Also==
==See Also==
*[[Thioredoxin]]
*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
 
*[[Thioredoxin 3D structures|Thioredoxin 3D structures]]
==Reference==
== References ==
<ref group="xtra">PMID:15528277</ref><references group="xtra"/>
<references/>
[[Category: DNA-directed DNA polymerase]]
__TOC__
[[Category: Enterobacteria phage t7]]
</StructureSection>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
[[Category: Dutta, S.]]
[[Category: Escherichia phage T7]]
[[Category: Dzantiev, L.]]
[[Category: Large Structures]]
[[Category: Ellenberger, T.]]
[[Category: Dutta S]]
[[Category: Johnson, D.]]
[[Category: Dzantiev L]]
[[Category: Li, Y.]]
[[Category: Ellenberger T]]
[[Category: Richardson, C C.]]
[[Category: Johnson D]]
[[Category: Romano, L J.]]
[[Category: Li Y]]
[[Category: Dna polymerase]]
[[Category: Richardson CC]]
[[Category: Mutagenesis]]
[[Category: Romano LJ]]
[[Category: N-2-aminofluorene]]
[[Category: Replication block]]
[[Category: Transferase/electron transport/dna complex]]

Latest revision as of 11:48, 14 February 2024

T7 DNA polymerase in complex with a primer/template DNA containing a disordered N-2 aminofluorene on the template, crystallized with dideoxy-CTP as the incoming nucleotide.T7 DNA polymerase in complex with a primer/template DNA containing a disordered N-2 aminofluorene on the template, crystallized with dideoxy-CTP as the incoming nucleotide.

Structural highlights

1x9s is a 4 chain structure with sequence from Escherichia coli and Escherichia phage T7. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.7Å
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

1x9s, resolution 2.70Å

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