We apologize for Proteopedia being slow to respond. For the past two years, a new implementation of Proteopedia has been being built. Soon, it will replace this 18-year old system. All existing content will be moved to the new system at a date that will be announced here.

9lm3

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

cryo-EM structure of retron Eco2

Structural highlights

9lm3 is a 15 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Electron Microscopy, Resolution 2.6Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RT67_ECOLX Reverse transcriptase (RT) component of antiviral defense system retron Ec67, minimally composed of a non-coding RNA (ncRNA) and this RT. Expression of these 2 elements confers protection against bacteriophage T5. At multiplicity of infection (MOI) of 0.02 cultures grow normally when infected with T5 without collapsing, at MOI 2 cultures enter growth stasis (PubMed:33157039). Responsible for synthesis of msDNA-Ec67 (a branched molecule with RNA linked by a 2',5'-phosphodiester bond to ssDNA). The retron transcript serves as primer (from a conserved internal G residue) and template for the reaction, and codes for the RT (PubMed:1378431, PubMed:1692831, PubMed:2466332). Can use other retrons as substrate (msDNA-Mx162 and msDNA-Ec86). Also able to synthesize DNA from a DNA template at least in vitro, although the enzyme is less active with a DNA template (PubMed:1692831).^[1] ^[2] ^[3] ^[4]

Publication Abstract from PubMed

In the evolutionary arms race between bacteria and viruses, retrons have emerged as distinctive antiphage defense systems. Here, we elucidate the structure and function of Retron-Eco2, which comprises a non-coding RNA (ncRNA) that encodes multicopy single-stranded DNA (msDNA, a DNAâRNA hybrid) and a fusion protein containing a reverse transcriptase (RT) domain and a topoisomerase-primase-like (Toprim) effector domain. The Eco2 msDNA and RT-Toprim fusion protein form a 1:1 stoichiometric nucleoprotein complex that further assembles into a trimer (msDNA:RT-Toprim ratio of 3:3) with a distinctive triangular configuration. The RNA portion of the msDNA in one protomer closely intertwines around the RT domain of an adjacent protomer, mediating the formation of this self-inhibitory assembly. Upon activation, the Toprim effector domain exhibits RNase activity, degrading RNA to arrest phage replication. We further reveal that phage mutants evading Eco2-mediated defense harbor mutations in the endonuclease IV-like protein DenB, underscoring DenB's critical role in triggering the activation of this system. Together, these findings provide key structural and functional insights into Retron-Eco2, laying the groundwork for harnessing its potential in biotechnology and synthetic biology applications.

Structural basis of the RNA-mediated Retron-Eco2 oligomerization.,Wang Y, Wang C, Yin Y, Cui Y, Dai Z, Liu C, Chen Y, Guan Z, Zou T Cell Discov. 2025 Sep 2;11(1):73. doi: 10.1038/s41421-025-00823-y. PMID:40897710^[5]

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

References

↑ Hsu MY, Eagle SG, Inouye M, Inouye S. Cell-free synthesis of the branched RNA-linked msDNA from retron-Ec67 of Escherichia coli. J Biol Chem. 1992 Jul 15;267(20):13823-9 PMID:1378431
↑ Lampson BC, Viswanathan M, Inouye M, Inouye S. Reverse transcriptase from Escherichia coli exists as a complex with msDNA and is able to synthesize double-stranded DNA. J Biol Chem. 1990 May 25;265(15):8490-6 PMID:1692831
↑ Lampson BC, Sun J, Hsu MY, Vallejo-Ramirez J, Inouye S, Inouye M. Reverse transcriptase in a clinical strain of Escherichia coli: production of branched RNA-linked msDNA. Science. 1989 Feb 24;243(4894 Pt 1):1033-8. PMID:2466332 doi:10.1126/science.2466332
↑ Millman A, Bernheim A, Stokar-Avihail A, Fedorenko T, Voichek M, Leavitt A, Oppenheimer-Shaanan Y, Sorek R. Bacterial Retrons Function In Anti-Phage Defense. Cell. 2020 Dec 10;183(6):1551-1561.e12. doi: 10.1016/j.cell.2020.09.065. Epub, 2020 Nov 5. PMID:33157039 doi:http://dx.doi.org/10.1016/j.cell.2020.09.065
↑ Wang Y, Wang C, Yin Y, Cui Y, Dai Z, Liu C, Chen Y, Guan Z, Zou T. Structural basis of the RNA-mediated Retron-Eco2 oligomerization. Cell Discov. 2025 Sep 2;11(1):73. PMID:40897710 doi:10.1038/s41421-025-00823-y

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/9lm3"

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 9lm3 is ON HOLD  until Paper Publication
+==cryo-EM structure of retron Eco2==
+<StructureSection load='9lm3' size='340' side='right'caption='[[9lm3]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[9lm3]] is a 15 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9LM3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9LM3 FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 2.6&#8491;</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=9lm3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9lm3 OCA], [https://pdbe.org/9lm3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9lm3 RCSB], [https://www.ebi.ac.uk/pdbsum/9lm3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9lm3 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RT67_ECOLX RT67_ECOLX] Reverse transcriptase (RT) component of antiviral defense system retron Ec67, minimally composed of a non-coding RNA (ncRNA) and this RT. Expression of these 2 elements confers protection against bacteriophage T5. At multiplicity of infection (MOI) of 0.02 cultures grow normally when infected with T5 without collapsing, at MOI 2 cultures enter growth stasis (PubMed:33157039). Responsible for synthesis of msDNA-Ec67 (a branched molecule with RNA linked by a 2',5'-phosphodiester bond to ssDNA). The retron transcript serves as primer (from a conserved internal G residue) and template for the reaction, and codes for the RT (PubMed:1378431, PubMed:1692831, PubMed:2466332). Can use other retrons as substrate (msDNA-Mx162 and msDNA-Ec86). Also able to synthesize DNA from a DNA template at least in vitro, although the enzyme is less active with a DNA template (PubMed:1692831).<ref>PMID:1378431</ref> <ref>PMID:1692831</ref> <ref>PMID:2466332</ref> <ref>PMID:33157039</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+In the evolutionary arms race between bacteria and viruses, retrons have emerged as distinctive antiphage defense systems. Here, we elucidate the structure and function of Retron-Eco2, which comprises a non-coding RNA (ncRNA) that encodes multicopy single-stranded DNA (msDNA, a DNAâRNA hybrid) and a fusion protein containing a reverse transcriptase (RT) domain and a topoisomerase-primase-like (Toprim) effector domain. The Eco2 msDNA and RT-Toprim fusion protein form a 1:1 stoichiometric nucleoprotein complex that further assembles into a trimer (msDNA:RT-Toprim ratio of 3:3) with a distinctive triangular configuration. The RNA portion of the msDNA in one protomer closely intertwines around the RT domain of an adjacent protomer, mediating the formation of this self-inhibitory assembly. Upon activation, the Toprim effector domain exhibits RNase activity, degrading RNA to arrest phage replication. We further reveal that phage mutants evading Eco2-mediated defense harbor mutations in the endonuclease IV-like protein DenB, underscoring DenB's critical role in triggering the activation of this system. Together, these findings provide key structural and functional insights into Retron-Eco2, laying the groundwork for harnessing its potential in biotechnology and synthetic biology applications.
-Authors:
+Structural basis of the RNA-mediated Retron-Eco2 oligomerization.,Wang Y, Wang C, Yin Y, Cui Y, Dai Z, Liu C, Chen Y, Guan Z, Zou T Cell Discov. 2025 Sep 2;11(1):73. doi: 10.1038/s41421-025-00823-y. PMID:40897710<ref>PMID:40897710</ref>
-Description:
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
+<div class="pdbe-citations 9lm3" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Escherichia coli]]
+[[Category: Large Structures]]
+[[Category: Guan ZY]]
+[[Category: Wang C]]
+[[Category: Wang YJ]]
+[[Category: Zou TT]]

9lm3

From Proteopedia

Current revision

cryo-EM structure of retron Eco2

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox