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1cr2

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CRYSTAL STRUCTURE OF THE HELICASE DOMAIN OF THE GENE 4 PROTEIN OF BACTERIOPHAGE T7: COMPLEX WITH DATP

Structural highlights

1cr2 is a 1 chain structure with sequence from 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 2.3Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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.

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

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1cr2"

@@ Line 1: / Line 1: @@
-[[Image:1cr2.gif|left|200px]]<br /><applet load="1cr2" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1cr2, resolution 2.30&Aring;" />
-'''CRYSTAL STRUCTURE OF THE HELICASE DOMAIN OF THE GENE 4 PROTEIN OF BACTERIOPHAGE T7: COMPLEX WITH DATP'''<br />
-==Overview==
+==CRYSTAL STRUCTURE OF THE HELICASE DOMAIN OF THE GENE 4 PROTEIN OF BACTERIOPHAGE T7: COMPLEX WITH DATP==
-Helicases that unwind DNA at the replication fork are ring-shaped, oligomeric enzymes that move along one strand of a DNA duplex and catalyze, the displacement of the complementary strand in a reaction that is coupled, to nucleotide hydrolysis. The helicase domain of the replicative, helicase-primase protein from bacteriophage T7 crystallized as a helical, filament that resembles the Escherichia coli RecA protein, an, ATP-dependent DNA strand exchange factor. When viewed in projection along, the helical axis of the crystals, six protomers of the T7 helicase domain, resemble the hexameric rings seen in electron microscopic images of the, intact T7 helicase-primase. Nucleotides bind at the interface between, pairs of adjacent subunits where an arginine is near the gamma-phosphate, of the nucleotide in trans. The bound nucleotide stabilizes the folded, conformation of a DNA-binding motif located near the center of the ring., These and other observations suggest how conformational changes are, coupled to DNA unwinding activity.
+<StructureSection load='1cr2' size='340' side='right'caption='[[1cr2]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1cr2]] is a 1 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=1CR2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1CR2 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]] 2.3&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DTP:2-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=1cr2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1cr2 OCA], [https://pdbe.org/1cr2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1cr2 RCSB], [https://www.ebi.ac.uk/pdbsum/1cr2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1cr2 ProSAT]</span></td></tr>
+</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 ==
+[[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/cr/1cr2_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=1cr2 ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-CR2 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacteriophage_t7 Bacteriophage t7] with SO4 and DTP as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1CR2 OCA].
+*[[RNA polymerase 3D structures|RNA polymerase 3D structures]]
+== References ==
-==Reference==
+<references/>
-Crystal structure of the helicase domain from the replicative helicase-primase of bacteriophage T7., Sawaya MR, Guo S, Tabor S, Richardson CC, Ellenberger T, Cell. 1999 Oct 15;99(2):167-77. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10535735 10535735]
+__TOC__
-[[Category: Bacteriophage t7]]
+</StructureSection>
-[[Category: Single protein]]
+[[Category: Escherichia phage T7]]
-[[Category: Ellenberger, T.]]
+[[Category: Large Structures]]
-[[Category: Guo, S.]]
+[[Category: Ellenberger T]]
-[[Category: Richardson, C.C.]]
+[[Category: Guo S]]
-[[Category: Sawaya, M.R.]]
+[[Category: Richardson CC]]
-[[Category: Tabor, S.]]
+[[Category: Sawaya MR]]
-[[Category: DTP]]
+[[Category: Tabor S]]
-[[Category: SO4]]
-[[Category: reca-type protein fold]]
-[[Category: transferase]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 12:41:32 2007''

1cr2

From Proteopedia

Current revision

CRYSTAL STRUCTURE OF THE HELICASE DOMAIN OF THE GENE 4 PROTEIN OF BACTERIOPHAGE T7: COMPLEX WITH DATP

Structural highlights

Function

Evolutionary Conservation

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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