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5ikn

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Revision as of 17:41, 15 November 2017

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Crystal Structure of the T7 Replisome in the Absence of DNA

Structural highlights

5ikn is a 13 chain structure with sequence from Bpt7 and Eco57. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Gene:	trxA, Z5291, ECs4714 (ECO57)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Warning: this is a large structure, and loading might take a long time or not happen at all.

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] [THIO_ECO57] Participates in various redox reactions through the reversible oxidation of its active center dithiol to a disulfide and catalyzes dithiol-disulfide exchange reactions (By similarity). [PRIM_BPT7] Synthesizes short RNA primers for DNA replication. Unwinds the DNA at the replication forks and generates single-stranded DNA for both leading and lagging strand synthesis. The primase synthesizes short RNA primers on the lagging strand that the polymerase elongates using dNTPs.^[3] ^[4] ^[5]

Publication Abstract from PubMed

The physical organization of DNA enzymes at a replication fork enables efficient copying of two antiparallel DNA strands, yet dynamic protein interactions within the replication complex complicate replisome structural studies. We employed a combination of crystallographic, native mass spectrometry and small-angle X-ray scattering experiments to capture alternative structures of a model replication system encoded by bacteriophage T7. Two molecules of DNA polymerase bind the ring-shaped primase-helicase in a conserved orientation and provide structural insight into how the acidic C-terminal tail of the primase-helicase contacts the DNA polymerase to facilitate loading of the polymerase onto DNA. A third DNA polymerase binds the ring in an offset manner that may enable polymerase exchange during replication. Alternative polymerase binding modes are also detected by small-angle X-ray scattering with DNA substrates present. Our collective results unveil complex motions within T7 replisome higher-order structures that are underpinned by multivalent protein-protein interactions with functional implications.

Hybrid Methods Reveal Multiple Flexibly Linked DNA Polymerases within the Bacteriophage T7 Replisome.,Wallen JR, Zhang H, Weis C, Cui W, Foster BM, Ho CM, Hammel M, Tainer JA, Gross ML, Ellenberger T Structure. 2017 Jan 3;25(1):157-166. doi: 10.1016/j.str.2016.11.019. PMID:28052235^[6]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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
↑ Kong D, Griffith JD, Richardson CC. Gene 4 helicase of bacteriophage T7 mediates strand transfer through pyrimidine dimers, mismatches, and nonhomologous regions. Proc Natl Acad Sci U S A. 1997 Apr 1;94(7):2987-92. PMID:9096333
↑ 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
↑ Kulczyk AW, Akabayov B, Lee SJ, Bostina M, Berkowitz SA, Richardson CC. An interaction between DNA polymerase and helicase is essential for the high processivity of the bacteriophage T7 replisome. J Biol Chem. 2012 Nov 9;287(46):39050-60. doi: 10.1074/jbc.M112.410647. Epub 2012, Sep 12. PMID:22977246 doi:http://dx.doi.org/10.1074/jbc.M112.410647
↑ Wallen JR, Zhang H, Weis C, Cui W, Foster BM, Ho CM, Hammel M, Tainer JA, Gross ML, Ellenberger T. Hybrid Methods Reveal Multiple Flexibly Linked DNA Polymerases within the Bacteriophage T7 Replisome. Structure. 2017 Jan 3;25(1):157-166. doi: 10.1016/j.str.2016.11.019. PMID:28052235 doi:http://dx.doi.org/10.1016/j.str.2016.11.019

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5ikn"

@@ Line 3: / Line 3: @@
 <StructureSection load='5ikn' size='340' side='right' caption='[[5ikn]], [[Resolution|resolution]] 4.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5ikn]] is a 13 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IKN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5IKN FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5ikn]] is a 13 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpt7 Bpt7] and [http://en.wikipedia.org/wiki/Eco57 Eco57]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IKN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5IKN FirstGlance]. <br>
-</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=5ikn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ikn OCA], [http://pdbe.org/5ikn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ikn RCSB], [http://www.ebi.ac.uk/pdbsum/5ikn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ikn ProSAT]</span></td></tr>
+</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">trxA, Z5291, ECs4714 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83334 ECO57])</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=5ikn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ikn OCA], [http://pdbe.org/5ikn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ikn RCSB], [http://www.ebi.ac.uk/pdbsum/5ikn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ikn ProSAT]</span></td></tr>
 </table>
 {{Large structure}}
@@ Line 22: / Line 23: @@
 __TOC__
 </StructureSection>
+[[Category: Bpt7]]
+[[Category: Eco57]]
 [[Category: Ellenberger, T]]
 [[Category: Wallen, J R]]
 [[Category: Replisome]]
 [[Category: Transferase]]

5ikn

From Proteopedia

Revision as of 17:41, 15 November 2017

Crystal Structure of the T7 Replisome in the Absence of DNA

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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