5mq9

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of Rae1 (YacP) from Bacillus subtilis (W164L mutant)

Structural highlights

5mq9 is a 2 chain structure with sequence from Bacillus subtilis subsp. subtilis str. 168. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 3.174Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

YACP_BACSU

Publication Abstract from PubMed

The PIN domain plays a central role in cellular RNA biology and is involved in processes as diverse as rRNA maturation, mRNA decay and telomerase function. Here, we solve the crystal structure of the Rae1 (YacP) protein of Bacillus subtilis, a founding member of the NYN (Nedd4-BP1/YacP nuclease) subfamily of PIN domain proteins, and identify potential substrates in vivo Unexpectedly, degradation of a characterised target mRNA was completely dependent on both its translation and reading frame. We provide evidence that Rae1 associates with the B. subtilis ribosome and cleaves between specific codons of this mRNA in vivo Critically, we also demonstrate translation-dependent Rae1 cleavage of this substrate in a purified translation assay in vitro Multiple lines of evidence converge to suggest that Rae1 is an A-site endoribonuclease. We present a docking model of Rae1 bound to the B. subtilis ribosomal A-site that is consistent with this hypothesis and show that Rae1 cleaves optimally immediately upstream of a lysine codon (AAA or AAG) in vivo.

Rae1/YacP, a new endoribonuclease involved in ribosome-dependent mRNA decay in Bacillus subtilis.,Leroy M, Piton J, Gilet L, Pellegrini O, Proux C, Coppee JY, Figaro S, Condon C EMBO J. 2017 Mar 31. pii: e201796540. doi: 10.15252/embj.201796540. PMID:28363943^[1]

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

References

↑ Leroy M, Piton J, Gilet L, Pellegrini O, Proux C, Coppee JY, Figaro S, Condon C. Rae1/YacP, a new endoribonuclease involved in ribosome-dependent mRNA decay in Bacillus subtilis. EMBO J. 2017 Mar 31. pii: e201796540. doi: 10.15252/embj.201796540. PMID:28363943 doi:http://dx.doi.org/10.15252/embj.201796540

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/5mq9"

@@ Line 1: / Line 1: @@
 ==Crystal structure of Rae1 (YacP) from Bacillus subtilis (W164L mutant)==
-<StructureSection load='5mq9' size='340' side='right' caption='[[5mq9]], [[Resolution|resolution]] 3.17&Aring;' scene=''>
+<StructureSection load='5mq9' size='340' side='right'caption='[[5mq9]], [[Resolution|resolution]] 3.17&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5mq9]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MQ9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5MQ9 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5mq9]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis_subsp._subtilis_str._168 Bacillus subtilis subsp. subtilis str. 168]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MQ9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5MQ9 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 3.174&#8491;</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=5mq9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mq9 OCA], [http://pdbe.org/5mq9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5mq9 RCSB], [http://www.ebi.ac.uk/pdbsum/5mq9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5mq9 ProSAT]</span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=5mq9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mq9 OCA], [https://pdbe.org/5mq9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5mq9 RCSB], [https://www.ebi.ac.uk/pdbsum/5mq9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5mq9 ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/YACP_BACSU YACP_BACSU]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 20: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Condon, C]]
+[[Category: Bacillus subtilis subsp. subtilis str. 168]]
-[[Category: Figaro, S]]
+[[Category: Large Structures]]
-[[Category: Gilet, L]]
+[[Category: Condon C]]
-[[Category: Leroy, M]]
+[[Category: Figaro S]]
-[[Category: Pellegrini, O]]
+[[Category: Gilet L]]
-[[Category: Piton, J]]
+[[Category: Leroy M]]
-[[Category: B. subtili]]
+[[Category: Pellegrini O]]
-[[Category: Endonuclease]]
+[[Category: Piton J]]
-[[Category: Peptide toxin]]
-[[Category: Rna maturation and decay]]
-[[Category: Translation]]

5mq9

From Proteopedia

Current revision

Crystal structure of Rae1 (YacP) from Bacillus subtilis (W164L mutant)

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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