This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

1is1

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

Crystal structure of ribosome recycling factor from Vibrio parahaemolyticus

Structural highlights

1is1 is a 1 chain structure with sequence from Vibrio parahaemolyticus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.2Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RRF_VIBPA Responsible for the release of ribosomes from messenger RNA at the termination of protein biosynthesis. May increase the efficiency of translation by recycling ribosomes from one round of translation to another.

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 and NMR analyses on ribosome recycling factors (RRFs) from thermophilic bacteria showed that they display a tRNA-like L-shaped conformation consisting of two domains. Since then, it has been accepted that domain I, consisting of a three-helix bundle, corresponds to the anticodon arm of tRNA and domain II and a beta/alpha/beta sandwich structure, corresponds to the acceptor arm. In this study, we obtained a RRF from a mesophilic bacterium, Vibrio parahaemolyticus, by gene cloning and carried out an x-ray analysis on it at 2.2 A resolution. This RRF was shown to be active in an in vitro assay system using Escherichia coli polysomes and elongation factor G (EF-G). In contrast, the above-mentioned RRFs from thermophilic bacteria were inactive in such a system. Analysis of the relative orientations between the two domains in the structures of various RRFs, including this RRF from mesophilic bacterium, revealed that domain II rotates about the long axis of the helix bundle of domain I. To elucidate the ribosome binding site of RRF, the peptide fragment (RRF-DI) corresponding to domain I of RRF was expressed and characterized. RRF-DI is bound to 70 S ribosome and the 50 S subunit with an affinity similar to that of wild-type RRF. But it does not bind to the 30 S subunit. These findings caused us to reinvestigate the concept of the mimicry of RRF to tRNA and to propose a new model where domain I corresponds to the acceptor arm of tRNA and domain II corresponds to the anticodon arm. This is just the reverse of a model that is now widely accepted. However, the new model is in better agreement with published biological findings.

Structure and binding mode of a ribosome recycling factor (RRF) from mesophilic bacterium.,Nakano H, Yoshida T, Uchiyama S, Kawachi M, Matsuo H, Kato T, Ohshima A, Yamaichi Y, Honda T, Kato H, Yamagata Y, Ohkubo T, Kobayashi Y J Biol Chem. 2003 Jan 31;278(5):3427-36. Epub 2002 Oct 30. PMID:12411440^[1]

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

References

↑ Nakano H, Yoshida T, Uchiyama S, Kawachi M, Matsuo H, Kato T, Ohshima A, Yamaichi Y, Honda T, Kato H, Yamagata Y, Ohkubo T, Kobayashi Y. Structure and binding mode of a ribosome recycling factor (RRF) from mesophilic bacterium. J Biol Chem. 2003 Jan 31;278(5):3427-36. Epub 2002 Oct 30. PMID:12411440 doi:10.1074/jbc.M208098200

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/1is1"

@@ Line 3: / Line 3: @@
 <StructureSection load='1is1' size='340' side='right'caption='[[1is1]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1is1]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"oceanomonas_parahaemolytica"_(fujino_et_al._1951)_miyamoto_et_al._1961 "oceanomonas parahaemolytica" (fujino et al. 1951) miyamoto et al. 1961]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IS1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1IS1 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1is1]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Vibrio_parahaemolyticus Vibrio parahaemolyticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IS1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IS1 FirstGlance]. <br>
-</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=1is1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1is1 OCA], [http://pdbe.org/1is1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1is1 RCSB], [http://www.ebi.ac.uk/pdbsum/1is1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1is1 ProSAT]</span></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]] 2.2&#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=1is1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1is1 OCA], [https://pdbe.org/1is1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1is1 RCSB], [https://www.ebi.ac.uk/pdbsum/1is1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1is1 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/RRF_VIBPA RRF_VIBPA]] Responsible for the release of ribosomes from messenger RNA at the termination of protein biosynthesis. May increase the efficiency of translation by recycling ribosomes from one round of translation to another.
+[https://www.uniprot.org/uniprot/RRF_VIBPA RRF_VIBPA] Responsible for the release of ribosomes from messenger RNA at the termination of protein biosynthesis. May increase the efficiency of translation by recycling ribosomes from one round of translation to another.
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 35: / Line 36: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Honda, T]]
+[[Category: Vibrio parahaemolyticus]]
-[[Category: Kato, H]]
+[[Category: Honda T]]
-[[Category: Kobayashi, Y]]
+[[Category: Kato H]]
-[[Category: Nakano, H]]
+[[Category: Kobayashi Y]]
-[[Category: Nishina, K]]
+[[Category: Nakano H]]
-[[Category: Ohkubo, T]]
+[[Category: Nishina K]]
-[[Category: Uchiyama, S]]
+[[Category: Ohkubo T]]
-[[Category: Yamagata, Y]]
+[[Category: Uchiyama S]]
-[[Category: Yamaichi, Y]]
+[[Category: Yamagata Y]]
-[[Category: Yoshida, T]]
+[[Category: Yamaichi Y]]
-[[Category: Translation]]
+[[Category: Yoshida T]]

1is1

From Proteopedia

Current revision

Crystal structure of ribosome recycling factor from Vibrio parahaemolyticus

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox