1skr: Difference between revisions

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New page: left|200px<br /><applet load="1skr" size="450" color="white" frame="true" align="right" spinBox="true" caption="1skr, resolution 2.4Å" /> '''T7 DNA Polymerase Com...
 
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[[Image:1skr.gif|left|200px]]<br /><applet load="1skr" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1skr, resolution 2.4&Aring;" />
'''T7 DNA Polymerase Complexed To DNA Primer/Template and ddATP'''<br />


==Overview==
==T7 DNA Polymerase Complexed To DNA Primer/Template and ddATP==
Ultraviolet-induced DNA damage poses a lethal block to replication. To, understand the structural basis for this, we determined crystal structures, of a replicative DNA polymerase from bacteriophage T7 in complex with, nucleotide substrates and a DNA template containing a cis-syn cyclobutane, pyrimidine dimer (CPD). When the 3' thymine is the templating base, the, CPD is rotated out of the polymerase active site and the fingers subdomain, adopts an open orientation. When the 5' thymine is the templating base, the CPD lies within the polymerase active site where it base-pairs with, the incoming nucleotide and the 3' base of the primer, while the fingers, are in a closed conformation. These structures reveal the basis for the, strong block of DNA replication that is caused by this photolesion.
<StructureSection load='1skr' size='340' side='right'caption='[[1skr]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1skr]] 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=1SKR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SKR 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]] 2.4&#8491;</td></tr>
<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></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=1skr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1skr OCA], [https://pdbe.org/1skr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1skr RCSB], [https://www.ebi.ac.uk/pdbsum/1skr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1skr 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/sk/1skr_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=1skr ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
1SKR is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Bacteriophage_t7 Bacteriophage t7] and [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with MG and DAD as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1SKR OCA].
*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
 
*[[Thioredoxin 3D structures|Thioredoxin 3D structures]]
==Reference==
== References ==
Nucleotide insertion opposite a cis-syn thymine dimer by a replicative DNA polymerase from bacteriophage T7., Li Y, Dutta S, Doublie S, Bdour HM, Taylor JS, Ellenberger T, Nat Struct Mol Biol. 2004 Aug;11(8):784-90. Epub 2004 Jul 4. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15235589 15235589]
<references/>
[[Category: Bacteriophage t7]]
__TOC__
[[Category: DNA-directed DNA polymerase]]
</StructureSection>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
[[Category: Protein complex]]
[[Category: Escherichia phage T7]]
[[Category: Bdour, H.M.]]
[[Category: Large Structures]]
[[Category: Doublie, S.]]
[[Category: Bdour HM]]
[[Category: Dutta, S.]]
[[Category: Doublie S]]
[[Category: Ellenberger, T.]]
[[Category: Dutta S]]
[[Category: Li, Y.]]
[[Category: Ellenberger T]]
[[Category: Taylor, J.S.]]
[[Category: Li Y]]
[[Category: DAD]]
[[Category: Taylor JS]]
[[Category: MG]]
[[Category: close]]
[[Category: dna polymerase]]
[[Category: open]]
[[Category: replication]]
[[Category: uv-lesion]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 02:26:37 2007''

Latest revision as of 11:31, 14 February 2024

T7 DNA Polymerase Complexed To DNA Primer/Template and ddATPT7 DNA Polymerase Complexed To DNA Primer/Template and ddATP

Structural highlights

1skr 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 2.4Å
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

1skr, resolution 2.40Å

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