2pxb: Difference between revisions

Revision as of 10:21, 13 February 2019

Variant 2 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle

Structural highlights

2pxb is a 2 chain structure with sequence from "bacillus_coli"_migula_1895 "bacillus coli" migula 1895. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	NCO
NonStd Res:	MSE
Related:	1dul
Gene:	ffh ("Bacillus coli" Migula 1895)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[SRP54_ECOLI] Involved in targeting and insertion of nascent membrane proteins into the cytoplasmic membrane. Binds to the hydrophobic signal sequence of the ribosome-nascent chain (RNC) as it emerges from the ribosomes. The SRP-RNC complex is then targeted to the cytoplasmic membrane where it interacts with the SRP receptor FtsY. Interaction with FtsY 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] ^[7]

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

X-ray crystallography of biologically important RNA molecules has been hampered by technical challenges, including finding heavy-atom derivatives to obtain high-quality experimental phase information. Existing techniques have drawbacks, limiting the rate at which important new structures are solved. To address this, we have developed a reliable means to localize heavy atoms specifically to virtually any RNA. By solving the crystal structures of thirteen variants of the G*U wobble pair cation binding motif, we have identified a version that when inserted into an RNA helix introduces a high-occupancy cation binding site suitable for phasing. This "directed soaking" strategy can be integrated fully into existing RNA crystallography methods, potentially increasing the rate at which important structures are solved and facilitating routine solving of structures using Cu-Kalpha radiation. This method already has been used to solve several crystal structures.

A general strategy to solve the phase problem in RNA crystallography.,Keel AY, Rambo RP, Batey RT, Kieft JS Structure. 2007 Jul;15(7):761-72. PMID:17637337^[8]

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

References

↑ Ribes V, Romisch K, Giner A, Dobberstein B, Tollervey D. E. coli 4.5S RNA is part of a ribonucleoprotein particle that has properties related to signal recognition particle. Cell. 1990 Nov 2;63(3):591-600. PMID:2171778
↑ Luirink J, High S, Wood H, Giner A, Tollervey D, Dobberstein B. Signal-sequence recognition by an Escherichia coli ribonucleoprotein complex. Nature. 1992 Oct 22;359(6397):741-3. PMID:1279430 doi:https://dx.doi.org/10.1038/359741a0
↑ Phillips GJ, Silhavy TJ. The E. coli ffh gene is necessary for viability and efficient protein export. Nature. 1992 Oct 22;359(6397):744-6. PMID:1331806 doi:https://dx.doi.org/10.1038/359744a0
↑ 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
↑ Froderberg L, Houben EN, Baars L, Luirink J, de Gier JW. Targeting and translocation of two lipoproteins in Escherichia coli via the SRP/Sec/YidC pathway. J Biol Chem. 2004 Jul 23;279(30):31026-32. Epub 2004 May 12. PMID:15140892 doi:10.1074/jbc.M403229200
↑ Keel AY, Rambo RP, Batey RT, Kieft JS. A general strategy to solve the phase problem in RNA crystallography. Structure. 2007 Jul;15(7):761-72. PMID:17637337 doi:10.1016/j.str.2007.06.003

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Ribes V, Romisch K, Giner A, Dobberstein B, Tollervey D. E. coli 4.5S RNA is part of a ribonucleoprotein particle that has properties related to signal recognition particle. Cell. 1990 Nov 2;63(3):591-600. PMID:2171778

[2] Luirink J, High S, Wood H, Giner A, Tollervey D, Dobberstein B. Signal-sequence recognition by an Escherichia coli ribonucleoprotein complex. Nature. 1992 Oct 22;359(6397):741-3. PMID:1279430 doi:https://dx.doi.org/10.1038/359741a0

[3] Phillips GJ, Silhavy TJ. The E. coli ffh gene is necessary for viability and efficient protein export. Nature. 1992 Oct 22;359(6397):744-6. PMID:1331806 doi:https://dx.doi.org/10.1038/359744a0

[4] 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

[5] 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

[6] 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

[7] Froderberg L, Houben EN, Baars L, Luirink J, de Gier JW. Targeting and translocation of two lipoproteins in Escherichia coli via the SRP/Sec/YidC pathway. J Biol Chem. 2004 Jul 23;279(30):31026-32. Epub 2004 May 12. PMID:15140892 doi:10.1074/jbc.M403229200

[8] Keel AY, Rambo RP, Batey RT, Kieft JS. A general strategy to solve the phase problem in RNA crystallography. Structure. 2007 Jul;15(7):761-72. PMID:17637337 doi:10.1016/j.str.2007.06.003

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@@ Line 3: / Line 3: @@
 <StructureSection load='2pxb' size='340' side='right' caption='[[2pxb]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2pxb]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PXB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PXB FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2pxb]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PXB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PXB FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</scene></td></tr>
 <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1dul|1dul]]</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ffh ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
 <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2pxb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pxb OCA], [http://pdbe.org/2pxb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2pxb RCSB], [http://www.ebi.ac.uk/pdbsum/2pxb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2pxb ProSAT]</span></td></tr>
 </table>
@@ Line 15: / Line 16: @@
 Check<jmol>
    <jmolCheckbox>
-     <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/px/2pxb_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/px/2pxb_consurf.spt"</scriptWhenChecked>
      <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 37: / Line 38: @@
 __TOC__
 </StructureSection>
+[[Category: Bacillus coli migula 1895]]
 [[Category: Batey, R T]]
 [[Category: Keel, A Y]]

2pxb: Difference between revisions

Revision as of 10:21, 13 February 2019

Variant 2 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

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