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| | <StructureSection load='6p7e' size='340' side='right'caption='[[6p7e]], [[Resolution|resolution]] 3.00Å' scene=''> | | <StructureSection load='6p7e' size='340' side='right'caption='[[6p7e]], [[Resolution|resolution]] 3.00Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6p7e]] is a 19 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6P7E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6P7E FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6p7e]] is a 19 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=6P7E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6P7E FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TTP:THYMIDINE-5-TRIPHOSPHATE'>TTP</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.001Å</td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6p7e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6p7e OCA], [http://pdbe.org/6p7e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6p7e RCSB], [http://www.ebi.ac.uk/pdbsum/6p7e PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6p7e ProSAT]</span></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=6p7e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6p7e OCA], [https://pdbe.org/6p7e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6p7e RCSB], [https://www.ebi.ac.uk/pdbsum/6p7e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6p7e ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://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> | + | [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> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </div> | | </div> |
| | <div class="pdbe-citations 6p7e" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 6p7e" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[DNA polymerase 3D structures|DNA polymerase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| | + | [[Category: Escherichia coli]] |
| | + | [[Category: Escherichia phage T7]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Bintz, B J]] | + | [[Category: Bintz BJ]] |
| - | [[Category: Ellenberger, T]] | + | [[Category: Ellenberger T]] |
| - | [[Category: Foster, B M]] | + | [[Category: Foster BM]] |
| - | [[Category: Gainey, M D]] | + | [[Category: Gainey MD]] |
| - | [[Category: Hammel, M]] | + | [[Category: Hammel M]] |
| - | [[Category: Rosenberg, D]] | + | [[Category: Rosenberg D]] |
| - | [[Category: Salvo, H]] | + | [[Category: Salvo H]] |
| - | [[Category: Stephens, K L]] | + | [[Category: Stephens KL]] |
| - | [[Category: Wallen, J R]] | + | [[Category: Wallen JR]] |
| - | [[Category: Dna binding protein]]
| + | |
| - | [[Category: Dna polymerase]]
| + | |
| - | [[Category: Dna replication]]
| + | |
| - | [[Category: Transferase-dna binding protein-dna complex]]
| + | |
| Structural highlights
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]
Publication Abstract from PubMed
Recent structural studies of the bacteriophage T7 DNA replication system have shed light on how multiple proteins assemble to copy two antiparallel DNA strands. In T7, acidic C-terminal tails of both the primase-helicase and single-stranded DNA binding protein bind to two basic patches on the DNA polymerase to aid in replisome assembly, processivity, and coordinated DNA synthesis. Although these electrostatic interactions are essential for DNA replication, the molecular details for how these tails bind the polymerase are unknown. We have determined an X-ray crystal structure of the T7 DNA polymerase bound to both a primer/template DNA and a peptide that mimics the C-terminal tail of the primase-helicase. The structure reveals that the essential C-terminal phenylalanine of the tail binds to a hydrophobic pocket that is surrounded by positive charge on the surface of the polymerase. We show that alterations of polymerase residues that engage the tail lead to defects in viral replication. In the structure, we also observe dTTP bound in the exonuclease active site and stacked against tryptophan 160. Using both primer/extension assays and high-throughput sequencing, we show how mutations in the exonuclease active site lead to defects in mismatch repair and an increase in the level of mutagenesis of the T7 genome. Finally, using small-angle X-ray scattering, we provide the first solution structures of a complex between the single-stranded DNA binding protein and the DNA polymerase and show how a single-stranded DNA binding protein dimer engages both one and two copies of DNA polymerase.
Combined Solution and Crystal Methods Reveal the Electrostatic Tethers That Provide a Flexible Platform for Replication Activities in the Bacteriophage T7 Replisome.,Foster BM, Rosenberg D, Salvo H, Stephens KL, Bintz BJ, Hammel M, Ellenberger T, Gainey MD, Wallen JR Biochemistry. 2019 Nov 12;58(45):4466-4479. doi: 10.1021/acs.biochem.9b00525., Epub 2019 Nov 4. PMID:31659895[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ 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
- ↑ 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
- ↑ Foster BM, Rosenberg D, Salvo H, Stephens KL, Bintz BJ, Hammel M, Ellenberger T, Gainey MD, Wallen JR. Combined Solution and Crystal Methods Reveal the Electrostatic Tethers That Provide a Flexible Platform for Replication Activities in the Bacteriophage T7 Replisome. Biochemistry. 2019 Nov 12;58(45):4466-4479. doi: 10.1021/acs.biochem.9b00525., Epub 2019 Nov 4. PMID:31659895 doi:http://dx.doi.org/10.1021/acs.biochem.9b00525
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