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| - | ==GP4D HELICASE FROM PHAGE T7 ADPNP COMPLEX== | + | |
| - | <StructureSection load='1e0j' size='340' side='right' caption='[[1e0j]], [[Resolution|resolution]] 3.00Å' scene=''> | + | ==gp4d helicase from phage T7 ADPNP complex== |
| | + | <StructureSection load='1e0j' size='340' side='right'caption='[[1e0j]], [[Resolution|resolution]] 3.00Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1e0j]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t7 Enterobacteria phage t7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1E0J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1E0J FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1e0j]] is a 6 chain structure with sequence from [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=1E0J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1E0J FirstGlance]. <br> |
| - | </td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><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]] 3Å</td></tr> |
| - | <tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1e0k|1e0k]], [[1b79|1b79]], [[1jwe|1jwe]], [[1cr0|1cr0]], [[1cr1|1cr1]], [[1cr2|1cr2]], [[1cr4|1cr4]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr> |
| - | <tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">GENE 4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10760 Enterobacteria phage T7])</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=1e0j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e0j OCA], [https://pdbe.org/1e0j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1e0j RCSB], [https://www.ebi.ac.uk/pdbsum/1e0j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1e0j ProSAT]</span></td></tr> |
| - | <tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1e0j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e0j OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1e0j RCSB], [http://www.ebi.ac.uk/pdbsum/1e0j PDBsum]</span></td></tr> | + | </table> |
| - | <table> | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/HELIC_BPT7 HELIC_BPT7] ATP-dependent DNA helicase and primase essential for viral DNA replication and recombination (PubMed:21606333, PubMed:22977246, PubMed:32009150). The helicase moves 5' -> 3' on the lagging strand template, unwinding the DNA duplex ahead of the leading strand polymerase at the replication fork and generating ssDNA for both leading and lagging strand synthesis (PubMed:21606333, PubMed:22977246, PubMed:32009150). ATP or dTTP hydrolysis propels each helicase domain to translocate 2 nt per step sequentially along DNA (PubMed:30679383, PubMed:17604719). Mediates strand transfer when a joint molecule is available and participates in recombinational DNA repair through its role in strand exchange (PubMed:9096333, PubMed:8617248). Primase activity synthesizes short RNA primers at the sequence 5'-GTC-3' on the lagging strand that the polymerase elongates using dNTPs and providing the primase is still present (PubMed:6454135, PubMed:9139692).[HAMAP-Rule:MF_04154]<ref>PMID:17604719</ref> <ref>PMID:21606333</ref> <ref>PMID:22977246</ref> <ref>PMID:30679383</ref> <ref>PMID:32009150</ref> <ref>PMID:6454135</ref> <ref>PMID:8617248</ref> <ref>PMID:9096333</ref> <ref>PMID:9139692</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| | Check<jmol> | | Check<jmol> |
| | <jmolCheckbox> | | <jmolCheckbox> |
| - | <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/e0/1e0j_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/e0/1e0j_consurf.spt"</scriptWhenChecked> |
| | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
| | </jmolCheckbox> | | </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/chain_selection.php?pdb_ID=2ata ConSurf]. | + | </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=1e0j ConSurf]. |
| | <div style="clear:both"></div> | | <div style="clear:both"></div> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
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| | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | </div> | | </div> |
| | + | <div class="pdbe-citations 1e0j" style="background-color:#fffaf0;"></div> |
| | | | |
| | ==See Also== | | ==See Also== |
| - | *[[Helicase|Helicase]] | + | *[[Helicase 3D structures|Helicase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Enterobacteria phage t7]] | + | [[Category: Escherichia phage T7]] |
| - | [[Category: Ellenberger, T.]] | + | [[Category: Large Structures]] |
| - | [[Category: Sawaya, M R.]] | + | [[Category: Ellenberger T]] |
| - | [[Category: Singleton, M R.]] | + | [[Category: Sawaya MR]] |
| - | [[Category: Wigley, D B.]] | + | [[Category: Singleton MR]] |
| - | [[Category: Atpase]] | + | [[Category: Wigley DB]] |
| - | [[Category: Dna replication]]
| + | |
| - | [[Category: Helicase]]
| + | |
| Structural highlights
Function
HELIC_BPT7 ATP-dependent DNA helicase and primase essential for viral DNA replication and recombination (PubMed:21606333, PubMed:22977246, PubMed:32009150). The helicase moves 5' -> 3' on the lagging strand template, unwinding the DNA duplex ahead of the leading strand polymerase at the replication fork and generating ssDNA for both leading and lagging strand synthesis (PubMed:21606333, PubMed:22977246, PubMed:32009150). ATP or dTTP hydrolysis propels each helicase domain to translocate 2 nt per step sequentially along DNA (PubMed:30679383, PubMed:17604719). Mediates strand transfer when a joint molecule is available and participates in recombinational DNA repair through its role in strand exchange (PubMed:9096333, PubMed:8617248). Primase activity synthesizes short RNA primers at the sequence 5'-GTC-3' on the lagging strand that the polymerase elongates using dNTPs and providing the primase is still present (PubMed:6454135, PubMed:9139692).[HAMAP-Rule:MF_04154][1] [2] [3] [4] [5] [6] [7] [8] [9]
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
We have determined the crystal structure of an active, hexameric fragment of the gene 4 helicase from bacteriophage T7. The structure reveals how subunit contacts stabilize the hexamer. Deviation from expected six-fold symmetry of the hexamer indicates that the structure is of an intermediate on the catalytic pathway. The structural consequences of the asymmetry suggest a "binding change" mechanism to explain how cooperative binding and hydrolysis of nucleotides are coupled to conformational changes in the ring that most likely accompany duplex unwinding. The structure of a complex with a nonhydrolyzable ATP analog provides additional evidence for this hypothesis, with only four of the six possible nucleotide binding sites being occupied in this conformation of the hexamer. This model suggests a mechanism for DNA translocation.
Crystal structure of T7 gene 4 ring helicase indicates a mechanism for sequential hydrolysis of nucleotides.,Singleton MR, Sawaya MR, Ellenberger T, Wigley DB Cell. 2000 Jun 9;101(6):589-600. PMID:10892646[10]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Johnson DS, Bai L, Smith BY, Patel SS, Wang MD. Single-molecule studies reveal dynamics of DNA unwinding by the ring-shaped T7 helicase. Cell. 2007 Jun 29;129(7):1299-309. PMID:17604719 doi:10.1016/j.cell.2007.04.038
- ↑ 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
- ↑ Gao Y, Cui Y, Fox T, Lin S, Wang H, de Val N, Zhou ZH, Yang W. Structures and operating principles of the replisome. Science. 2019 Feb 22;363(6429). pii: science.aav7003. doi:, 10.1126/science.aav7003. Epub 2019 Jan 24. PMID:30679383 doi:http://dx.doi.org/10.1126/science.aav7003
- ↑ Ma JB, Chen Z, Xu CH, Huang XY, Jia Q, Zou ZY, Mi CY, Ma DF, Lu Y, Zhang HD, Li M. Dynamic structural insights into the molecular mechanism of DNA unwinding by the bacteriophage T7 helicase. Nucleic Acids Res. 2020 Apr 6;48(6):3156-3164. PMID:32009150 doi:10.1093/nar/gkaa057
- ↑ Tabor S, Richardson CC. Template recognition sequence for RNA primer synthesis by gene 4 protein of bacteriophage T7. Proc Natl Acad Sci U S A. 1981 Jan;78(1):205-9. PMID:6454135 doi:10.1073/pnas.78.1.205
- ↑ Kong D, Richardson CC. Single-stranded DNA binding protein and DNA helicase of bacteriophage T7 mediate homologous DNA strand exchange. EMBO J. 1996 Apr 15;15(8):2010-9 PMID:8617248
- ↑ 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
- ↑ Kusakabe T, Richardson CC. Gene 4 DNA primase of bacteriophage T7 mediates the annealing and extension of ribo-oligonucleotides at primase recognition sites. J Biol Chem. 1997 May 9;272(19):12446-53. PMID:9139692 doi:10.1074/jbc.272.19.12446
- ↑ Singleton MR, Sawaya MR, Ellenberger T, Wigley DB. Crystal structure of T7 gene 4 ring helicase indicates a mechanism for sequential hydrolysis of nucleotides. Cell. 2000 Jun 9;101(6):589-600. PMID:10892646
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