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2vrh

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Revision as of 00:38, 9 February 2016

Structure of the E. coli trigger factor bound to a translating ribosome

Structural highlights

2vrh is a 4 chain structure with sequence from "bacillus_coli"_migula_1895 "bacillus coli" migula 1895 and Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
NonStd Res:
Related:	1p9y, 2j28, 2vhm, 2wwq, 1p86, 2aw4, 1w26, 1w2b, 1p85, 2vhn, 1oms, 2awb, 1l1p
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum

Function

[RL29_ECOLI] Binds 23S rRNA. It is not essential for growth.[HAMAP-Rule:MF_00374] One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit. Contacts trigger factor (PubMed:12226666).[HAMAP-Rule:MF_00374] [TIG_ECOLI] Involved in protein export. Acts as a chaperone by maintaining the newly synthesized secretory and non-secretory proteins in an open conformation. Binds to nascent polypeptide chains via ribosomal protein L23 (PubMed:12226666). Functions as a peptidyl-prolyl cis-trans isomerase in vitro, this activity is dispensible in vivo for chaperone activity.^[1] ^[2] ^[3] [RL24_ECOLI] One of two assembly initiator proteins, it binds directly to the 5'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit. It is not thought to be involved in the functions of the mature 50S subunit in vitro.^[4] One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit.^[5] [RL23_ECOL5] One of the early assembly proteins it binds 23S rRNA. One of the proteins that surrounds the polypeptide exit tunnel on the outside of the ribosome. Forms the main docking site for trigger factor binding to the ribosome (By similarity).

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

Ribosome-associated chaperone Trigger Factor (TF) initiates folding of newly synthesized proteins in bacteria. Here, we pinpoint by site-specific crosslinking the sequence of molecular interactions of Escherichia coli TF and nascent chains during translation. Furthermore, we provide the first full-length structure of TF associated with ribosome-nascent chain complexes by using cryo-electron microscopy. In its active state, TF arches over the ribosomal exit tunnel accepting nascent chains in a protective void. The growing nascent chain initially follows a predefined path through the entire interior of TF in an unfolded conformation, and even after folding into a domain it remains accommodated inside the protective cavity of ribosome-bound TF. The adaptability to accept nascent chains of different length and folding states may explain how TF is able to assist co-translational folding of all kinds of nascent polypeptides during ongoing synthesis. Moreover, we suggest a model of how TF's chaperoning function can be coordinated with the co-translational processing and membrane targeting of nascent polypeptides by other ribosome-associated factors.

Molecular mechanism and structure of Trigger Factor bound to the translating ribosome.,Merz F, Boehringer D, Schaffitzel C, Preissler S, Hoffmann A, Maier T, Rutkowska A, Lozza J, Ban N, Bukau B, Deuerling E EMBO J. 2008 Jun 4;27(11):1622-32. Epub 2008 May 22. PMID:18497744^[6]

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

References

↑ Hesterkamp T, Hauser S, Lutcke H, Bukau B. Escherichia coli trigger factor is a prolyl isomerase that associates with nascent polypeptide chains. Proc Natl Acad Sci U S A. 1996 Apr 30;93(9):4437-41. PMID:8633085
↑ Valent QA, Kendall DA, High S, Kusters R, Oudega B, Luirink J. Early events in preprotein recognition in E. coli: interaction of SRP and trigger factor with nascent polypeptides. EMBO J. 1995 Nov 15;14(22):5494-505. PMID:8521806
↑ Genevaux P, Keppel F, Schwager F, Langendijk-Genevaux PS, Hartl FU, Georgopoulos C. In vivo analysis of the overlapping functions of DnaK and trigger factor. EMBO Rep. 2004 Feb;5(2):195-200. Epub 2004 Jan 9. PMID:14726952 doi:10.1038/sj.embor.7400067
↑ Spillmann S, Nierhaus KH. The ribosomal protein L24 of Escherichia coli is an assembly protein. J Biol Chem. 1978 Oct 10;253(19):7047-50. PMID:357435
↑ Spillmann S, Nierhaus KH. The ribosomal protein L24 of Escherichia coli is an assembly protein. J Biol Chem. 1978 Oct 10;253(19):7047-50. PMID:357435
↑ Merz F, Boehringer D, Schaffitzel C, Preissler S, Hoffmann A, Maier T, Rutkowska A, Lozza J, Ban N, Bukau B, Deuerling E. Molecular mechanism and structure of Trigger Factor bound to the translating ribosome. EMBO J. 2008 Jun 4;27(11):1622-32. Epub 2008 May 22. PMID:18497744 doi:http://dx.doi.org/10.1038/emboj.2008.89

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2vrh"

@@ Line 2: / Line 2: @@
 <StructureSection load='2vrh' size='340' side='right' caption='[[2vrh]], [[Resolution|resolution]] 19.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2vrh]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VRH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2VRH FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2vrh]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895] and [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VRH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2VRH FirstGlance]. <br>
 </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">[[1p9y|1p9y]], [[2j28|2j28]], [[2vhm|2vhm]], [[2wwq|2wwq]], [[1p86|1p86]], [[2aw4|2aw4]], [[1w26|1w26]], [[1w2b|1w2b]], [[1p85|1p85]], [[2vhn|2vhn]], [[1oms|1oms]], [[2awb|2awb]], [[1l1p|1l1p]]</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=2vrh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vrh OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2vrh RCSB], [http://www.ebi.ac.uk/pdbsum/2vrh PDBsum]</span></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=2vrh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vrh OCA], [http://pdbe.org/2vrh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2vrh RCSB], [http://www.ebi.ac.uk/pdbsum/2vrh PDBsum]</span></td></tr>
 </table>
 == Function ==
@@ Line 17: / Line 17: @@
     <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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=2vrh ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 27: / Line 27: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 2vrh" style="background-color:#fffaf0;"></div>
 ==See Also==
+*[[Ribosomal protein L23|Ribosomal protein L23]]
 *[[Ribosomal protein L24|Ribosomal protein L24]]
 *[[Ribosomal protein L29|Ribosomal protein L29]]
@@ Line 35: / Line 37: @@
 __TOC__
 </StructureSection>
+[[Category: Bacillus coli migula 1895]]
 [[Category: Escherichia coli]]
 [[Category: Ban, N]]

2vrh

From Proteopedia

Revision as of 00:38, 9 February 2016

Structure of the E. coli trigger factor bound to a translating ribosome

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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