6cqp: Difference between revisions

Latest revision as of 15:09, 4 October 2023

High resolution crystal structure of FtsY-NG domain of E. coli

Structural highlights

6cqp is a 2 chain structure with sequence from Escherichia coli K-12. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.446Å
Ligands:	GOL, NA
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

FTSY_ECOLI Involved in targeting and insertion of nascent membrane proteins into the cytoplasmic membrane. Acts as a receptor for the complex formed by the signal recognition particle (SRP) and the ribosome-nascent chain (RNC). Interaction with SRP-RNC leads to the transfer of the RNC complex to the Sec translocase for insertion into the membrane, the hydrolysis of GTP by both Ffh and FtsY, and the dissociation of the SRP-FtsY complex into the individual components.^[1] ^[2] ^[3] ^[4] ^[5] ^[6]

Publication Abstract from PubMed

Given the increasing incidence of antibiotic resistance, antibiotics that employ new strategies are urgently needed. Bacterial survival is dependent on proper function of the signal recognition particle (SRP) and its receptor (FtsY). A unique set of interactions in FtsY:SRP-RNA represents a promising candidate for new antibiotic development as no antibiotic targets this complex and these interactions are functionally replaced by protein:protein interactions in eukaryotes. We used a Fragment Based Drug Design (FBDD) approach to search for new compounds that can bind FtsY, and have identified three lead fragments. In vitro and in vivo analyses have shown that despite a high micromolar binding affinity, one fragment has some antimicrobial properties. X-ray structures of E. coli FtsY:fragments reveal the fragments bind in the targeted RNA interaction site. Our results show that FBDD is a suitable approach for targeting FtsY:SRP-RNA for antibiotic development and opens the possibility of targeting protein:RNA interactions in general.

Discovery of fragments that target key interactions in the signal recognition particle (SRP) as potential leads for a new class of antibiotics.,Faoro C, Wilkinson-White L, Kwan AH, Ataide SF PLoS One. 2018 Jul 25;13(7):e0200387. doi: 10.1371/journal.pone.0200387., eCollection 2018. PMID:30044812^[7]

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

References

↑ Luirink J, ten Hagen-Jongman CM, van der Weijden CC, Oudega B, High S, Dobberstein B, Kusters R. An alternative protein targeting pathway in Escherichia coli: studies on the role of FtsY. EMBO J. 1994 May 15;13(10):2289-96. PMID:8194520
↑ Powers T, Walter P. Co-translational protein targeting catalyzed by the Escherichia coli signal recognition particle and its receptor. EMBO J. 1997 Aug 15;16(16):4880-6. PMID:9305630 doi:10.1093/emboj/16.16.4880
↑ Peluso P, Shan SO, Nock S, Herschlag D, Walter P. Role of SRP RNA in the GTPase cycles of Ffh and FtsY. Biochemistry. 2001 Dec 18;40(50):15224-33. PMID:11735405
↑ Tian H, Beckwith J. Genetic screen yields mutations in genes encoding all known components of the Escherichia coli signal recognition particle pathway. J Bacteriol. 2002 Jan;184(1):111-8. PMID:11741850
↑ Buskiewicz I, Deuerling E, Gu SQ, Jockel J, Rodnina MV, Bukau B, Wintermeyer W. Trigger factor binds to ribosome-signal-recognition particle (SRP) complexes and is excluded by binding of the SRP receptor. Proc Natl Acad Sci U S A. 2004 May 25;101(21):7902-6. Epub 2004 May 17. PMID:15148364 doi:https://dx.doi.org/10.1073/pnas.0402231101
↑ Shan SO, Chandrasekar S, Walter P. Conformational changes in the GTPase modules of the signal reception particle and its receptor drive initiation of protein translocation. J Cell Biol. 2007 Aug 13;178(4):611-20. Epub 2007 Aug 6. PMID:17682051 doi:https://dx.doi.org/10.1083/jcb.200702018
↑ Faoro C, Wilkinson-White L, Kwan AH, Ataide SF. Discovery of fragments that target key interactions in the signal recognition particle (SRP) as potential leads for a new class of antibiotics. PLoS One. 2018 Jul 25;13(7):e0200387. doi: 10.1371/journal.pone.0200387., eCollection 2018. PMID:30044812 doi:https://dx.doi.org/10.1371/journal.pone.0200387

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Luirink J, ten Hagen-Jongman CM, van der Weijden CC, Oudega B, High S, Dobberstein B, Kusters R. An alternative protein targeting pathway in Escherichia coli: studies on the role of FtsY. EMBO J. 1994 May 15;13(10):2289-96. PMID:8194520

[2] Powers T, Walter P. Co-translational protein targeting catalyzed by the Escherichia coli signal recognition particle and its receptor. EMBO J. 1997 Aug 15;16(16):4880-6. PMID:9305630 doi:10.1093/emboj/16.16.4880

[3] Peluso P, Shan SO, Nock S, Herschlag D, Walter P. Role of SRP RNA in the GTPase cycles of Ffh and FtsY. Biochemistry. 2001 Dec 18;40(50):15224-33. PMID:11735405

[4] Tian H, Beckwith J. Genetic screen yields mutations in genes encoding all known components of the Escherichia coli signal recognition particle pathway. J Bacteriol. 2002 Jan;184(1):111-8. PMID:11741850

[5] Buskiewicz I, Deuerling E, Gu SQ, Jockel J, Rodnina MV, Bukau B, Wintermeyer W. Trigger factor binds to ribosome-signal-recognition particle (SRP) complexes and is excluded by binding of the SRP receptor. Proc Natl Acad Sci U S A. 2004 May 25;101(21):7902-6. Epub 2004 May 17. PMID:15148364 doi:https://dx.doi.org/10.1073/pnas.0402231101

[6] Shan SO, Chandrasekar S, Walter P. Conformational changes in the GTPase modules of the signal reception particle and its receptor drive initiation of protein translocation. J Cell Biol. 2007 Aug 13;178(4):611-20. Epub 2007 Aug 6. PMID:17682051 doi:https://dx.doi.org/10.1083/jcb.200702018

[7] Faoro C, Wilkinson-White L, Kwan AH, Ataide SF. Discovery of fragments that target key interactions in the signal recognition particle (SRP) as potential leads for a new class of antibiotics. PLoS One. 2018 Jul 25;13(7):e0200387. doi: 10.1371/journal.pone.0200387., eCollection 2018. PMID:30044812 doi:https://dx.doi.org/10.1371/journal.pone.0200387

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[6]

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@@ Line 3: / Line 3: @@
 <StructureSection load='6cqp' size='340' side='right'caption='[[6cqp]], [[Resolution|resolution]] 1.45&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6cqp]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CQP OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6CQP FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6cqp]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CQP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6CQP FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.446&#8491;</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6cqp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cqp OCA], [http://pdbe.org/6cqp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6cqp RCSB], [http://www.ebi.ac.uk/pdbsum/6cqp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6cqp ProSAT]</span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=6cqp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cqp OCA], [https://pdbe.org/6cqp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6cqp RCSB], [https://www.ebi.ac.uk/pdbsum/6cqp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6cqp ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/FTSY_ECOLI FTSY_ECOLI]] Involved in targeting and insertion of nascent membrane proteins into the cytoplasmic membrane. Acts as a receptor for the complex formed by the signal recognition particle (SRP) and the ribosome-nascent chain (RNC). Interaction with SRP-RNC leads to the transfer of the RNC complex to the Sec translocase for insertion into the membrane, the hydrolysis of GTP by both Ffh and FtsY, and the dissociation of the SRP-FtsY complex into the individual components.<ref>PMID:8194520</ref> <ref>PMID:9305630</ref> <ref>PMID:11735405</ref> <ref>PMID:11741850</ref> <ref>PMID:15148364</ref> <ref>PMID:17682051</ref>
+[https://www.uniprot.org/uniprot/FTSY_ECOLI FTSY_ECOLI] Involved in targeting and insertion of nascent membrane proteins into the cytoplasmic membrane. Acts as a receptor for the complex formed by the signal recognition particle (SRP) and the ribosome-nascent chain (RNC). Interaction with SRP-RNC leads to the transfer of the RNC complex to the Sec translocase for insertion into the membrane, the hydrolysis of GTP by both Ffh and FtsY, and the dissociation of the SRP-FtsY complex into the individual components.<ref>PMID:8194520</ref> <ref>PMID:9305630</ref> <ref>PMID:11735405</ref> <ref>PMID:11741850</ref> <ref>PMID:15148364</ref> <ref>PMID:17682051</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 25: / Line 26: @@
 __TOC__
 </StructureSection>
+[[Category: Escherichia coli K-12]]
 [[Category: Large Structures]]
-[[Category: Ataide, S F]]
+[[Category: Ataide SF]]
-[[Category: Faoro, C]]
+[[Category: Faoro C]]
-[[Category: Cotranslational delivery srp]]
-[[Category: Protein transport]]

6cqp: Difference between revisions

Latest revision as of 15:09, 4 October 2023

High resolution crystal structure of FtsY-NG domain of E. coli

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

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