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8dvf

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T4 Bacteriophage primosome with single strand DNA, state 1

Structural highlights

8dvf is a 9 chain structure with sequence from Escherichia phage T4. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Electron Microscopy, Resolution 3.3Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

HELIC_BPT4 ATP-dependent DNA helicase essential for viral DNA replication and recombination (PubMed:10871615). 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:11459969, PubMed:23578280). Interaction with the primase allows the primase to initiate lagging strand synthesis and fully activates the helicase (PubMed:22869700, PubMed:23578280). Loaded by the helicase assembly factor on replication forks that begin at discrete replication origin sequences, as well as on forks that are created during recombination (PubMed:10871615).[HAMAP-Rule:MF_04155]^[1] ^[2] ^[3] ^[4]

Publication Abstract from PubMed

The T4 bacteriophage gp41 helicase and gp61 primase assemble into a primosome complex to couple DNA unwinding with RNA primer synthesis for DNA replication. How a primosome is assembled and how the length of the RNA primer is defined in the T4 bacteriophage, or in any model system, are unclear. Here we report a series of cryo-EM structures of T4 primosome assembly intermediates at resolutions up to 2.7 A. We show that the gp41 helicase is an open spiral in the absence of ssDNA, and ssDNA binding triggers a large-scale scissor-like conformational change that drives the open spiral to a closed ring that activates the helicase. We found that the activation of the gp41 helicase exposes a cryptic hydrophobic primase-binding surface allowing for the recruitment of the gp61 primase. The primase binds the gp41 helicase in a bipartite mode in which the N-terminal Zn-binding domain (ZBD) and the C-terminal RNA polymerase domain (RPD) each contain a helicase-interacting motif (HIM1 and HIM2, respectively) that bind to separate gp41 N-terminal hairpin dimers, leading to the assembly of one primase on the helicase hexamer. Based on two observed primosome conformations - one in a DNA-scanning mode and the other in a post RNA primer-synthesis mode - we suggest that the linker loop between the gp61 ZBD and RPD contributes to the T4 pentaribonucleotide primer. Our study reveals T4 primosome assembly process and sheds light on RNA primer synthesis mechanism.

Structural basis of the T4 bacteriophage primosome assembly and primer synthesis.,Feng X, Spiering MM, de Luna Almeida Santos R, Benkovic SJ, Li H bioRxiv. 2023 May 3:2023.05.03.539249. doi: 10.1101/2023.05.03.539249. Preprint. PMID:37205424^[5]

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

References

↑ Jones CE, Mueser TC, Nossal NG. Interaction of the bacteriophage T4 gene 59 helicase loading protein and gene 41 helicase with each other and with fork, flap, and cruciform DNA. J Biol Chem. 2000 Sep 1;275(35):27145-54. PMID:10871615 doi:10.1074/jbc.M003808200
↑ Jose D, Weitzel SE, Jing D, von Hippel PH. Assembly and subunit stoichiometry of the functional helicase-primase (primosome) complex of bacteriophage T4. Proc Natl Acad Sci U S A. 2012 Aug 21;109(34):13596-601. PMID:22869700 doi:10.1073/pnas.1210040109
↑ Lee W, Jose D, Phelps C, Marcus AH, von Hippel PH. A single-molecule view of the assembly pathway, subunit stoichiometry, and unwinding activity of the bacteriophage T4 primosome (helicase-primase) complex. Biochemistry. 2013 May 7;52(18):3157-70. PMID:23578280 doi:10.1021/bi400231s
↑ Jones CE, Mueser TC, Dudas KC, Kreuzer KN, Nossal NG. Bacteriophage T4 gene 41 helicase and gene 59 helicase-loading protein: a versatile couple with roles in replication and recombination. Proc Natl Acad Sci U S A. 2001 Jul 17;98(15):8312-8. PMID:11459969 doi:10.1073/pnas.121009398
↑ Feng X, Spiering MM, de Luna Almeida Santos R, Benkovic SJ, Li H. Structural basis of the T4 bacteriophage primosome assembly and primer synthesis. bioRxiv. 2023 May 3:2023.05.03.539249. PMID:37205424 doi:10.1101/2023.05.03.539249

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/8dvf"

Categories: Escherichia phage T4 | Large Structures | Feng X | Li H

@@ Line 4: / Line 4: @@
 == Structural highlights ==
 <table><tr><td colspan='2'>[[8dvf]] is a 9 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_phage_T4 Escherichia phage T4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8DVF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8DVF FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AGS:PHOSPHOTHIOPHOSPHORIC+ACID-ADENYLATE+ESTER'>AGS</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3.3&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AGS:PHOSPHOTHIOPHOSPHORIC+ACID-ADENYLATE+ESTER'>AGS</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=8dvf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8dvf OCA], [https://pdbe.org/8dvf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8dvf RCSB], [https://www.ebi.ac.uk/pdbsum/8dvf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8dvf ProSAT]</span></td></tr>
 </table>

8dvf

From Proteopedia

Current revision

T4 Bacteriophage primosome with single strand DNA, state 1

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

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