3zq4

From Proteopedia

(Difference between revisions)

Current revision

Unusual, dual endo- and exo-nuclease activity in the degradosome explained by crystal structure analysis of RNase J1

Structural highlights

3zq4 is a 4 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 3Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RNJ1_BACSU An RNase that has endonuclease and 5'-3' exonuclease activity, playing a role in both rRNA and mRNA stability and degradation. Endonuclease activity can cleave within 4 nucleotides of the 5'-end of a triphosphorylated RNA. Endonuclease digestion by the RNase J1/J2 complex occurs at a different site and in some cases more efficiently than J1 or J2 alone. The exonuclease activity of the J1/J2 complex is highly processive on substrates longer than 5 nucleotides, on shorter substrates is distributive. Preferentially cleaves ssRNA, possibly in AU-rich regions. The 5'-exonuclease activity acts on 5'-hydroxyl and 5'-monophosphate but not 5'-triphosphate ends; it can digest through stem-loop structures if they are not too stable. Required for maturation of 16S rRNA. Acts preferentially on 16S rRNA precursors after association of the 30S and 50S ribosomal subunits. Plays a role in the secondary pathway of 23S rRNA 5' end maturation. Probably also participates in processing of pre-scRNA (the precursor of the signal recognition particle RNA).^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7] ^[8] ^[9] ^[10] ^[11] ^[12] ^[13]

Publication Abstract from PubMed

RNase J is an essential enzyme in Bacillus subtilis with unusual dual endonuclease and 5'-to-3' exonuclease activities that play an important role in the maturation and degradation of mRNA. RNase J is also a component of the recently identified "degradosome" of B. subtilis. We report the crystal structure of RNase J1 from B. subtilis to 3.0 A resolution, analysis of which reveals it to be in an open conformation suitable for binding substrate RNA. RNase J is a member of the beta-CASP family of zinc-dependent metallo-beta-lactamases. We have exploited this similarity in constructing a model for an RNase J1:RNA complex. Analysis of this model reveals candidate-stacking interactions with conserved aromatic side chains, providing a molecular basis for the observed enzyme activity. Comparisons of the B. subtilis RNase J structure with related enzymes reveal key differences that provide insights into conformational changes during catalysis and the role of the C-terminal domain.

Unusual, Dual Endo- and Exonuclease Activity in the Degradosome Explained by Crystal Structure Analysis of RNase J1.,Newman JA, Hewitt L, Rodrigues C, Solovyova A, Harwood CR, Lewis RJ Structure. 2011 Sep 7;19(9):1241-51. PMID:21893285^[14]

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

References

↑ Even S, Pellegrini O, Zig L, Labas V, Vinh J, Brechemmier-Baey D, Putzer H. Ribonucleases J1 and J2: two novel endoribonucleases in B.subtilis with functional homology to E.coli RNase E. Nucleic Acids Res. 2005 Apr 14;33(7):2141-52. Print 2005. PMID:15831787 doi:http://dx.doi.org/10.1093/nar/gki505
↑ Britton RA, Wen T, Schaefer L, Pellegrini O, Uicker WC, Mathy N, Tobin C, Daou R, Szyk J, Condon C. Maturation of the 5' end of Bacillus subtilis 16S rRNA by the essential ribonuclease YkqC/RNase J1. Mol Microbiol. 2007 Jan;63(1):127-38. PMID:17229210 doi:http://dx.doi.org/10.1111/j.1365-2958.2006.05499.x
↑ Mathy N, Benard L, Pellegrini O, Daou R, Wen T, Condon C. 5'-to-3' exoribonuclease activity in bacteria: role of RNase J1 in rRNA maturation and 5' stability of mRNA. Cell. 2007 May 18;129(4):681-92. PMID:17512403 doi:http://dx.doi.org/10.1016/j.cell.2007.02.051
↑ Yao S, Blaustein JB, Bechhofer DH. Processing of Bacillus subtilis small cytoplasmic RNA: evidence for an additional endonuclease cleavage site. Nucleic Acids Res. 2007;35(13):4464-73. Epub 2007 Jun 18. PMID:17576666 doi:http://dx.doi.org/10.1093/nar/gkm460
↑ de la Sierra-Gallay IL, Zig L, Jamalli A, Putzer H. Structural insights into the dual activity of RNase J. Nat Struct Mol Biol. 2008 Feb;15(2):206-12. Epub 2008 Jan 20. PMID:18204464 doi:10.1038/nsmb.1376
↑ Deikus G, Condon C, Bechhofer DH. Role of Bacillus subtilis RNase J1 endonuclease and 5'-exonuclease activities in trp leader RNA turnover. J Biol Chem. 2008 Jun 20;283(25):17158-67. doi: 10.1074/jbc.M801461200. Epub 2008, Apr 29. PMID:18445592 doi:http://dx.doi.org/10.1074/jbc.M801461200
↑ Mader U, Zig L, Kretschmer J, Homuth G, Putzer H. mRNA processing by RNases J1 and J2 affects Bacillus subtilis gene expression on a global scale. Mol Microbiol. 2008 Oct;70(1):183-96. doi: 10.1111/j.1365-2958.2008.06400.x. Epub, 2008 Aug 18. PMID:18713320 doi:http://dx.doi.org/10.1111/j.1365-2958.2008.06400.x
↑ Redko Y, Condon C. Maturation of 23S rRNA in Bacillus subtilis in the absence of Mini-III. J Bacteriol. 2010 Jan;192(1):356-9. doi: 10.1128/JB.01096-09. Epub . PMID:19880604 doi:http://dx.doi.org/10.1128/JB.01096-09
↑ Mathy N, Hebert A, Mervelet P, Benard L, Dorleans A, Li de la Sierra-Gallay I, Noirot P, Putzer H, Condon C. Bacillus subtilis ribonucleases J1 and J2 form a complex with altered enzyme behaviour. Mol Microbiol. 2010 Jan;75(2):489-98. doi: 10.1111/j.1365-2958.2009.07004.x. Epub, 2009 Dec 16. PMID:20025672 doi:http://dx.doi.org/10.1111/j.1365-2958.2009.07004.x
↑ Dorleans A, Li de la Sierra-Gallay I, Piton J, Zig L, Gilet L, Putzer H, Condon C. Molecular basis for the recognition and cleavage of RNA by the bifunctional 5'-3' exo/endoribonuclease RNase J. Structure. 2011 Sep 7;19(9):1252-61. PMID:21893286 doi:10.1016/j.str.2011.06.018
↑ Taverniti V, Forti F, Ghisotti D, Putzer H. Mycobacterium smegmatis RNase J is a 5'-3' exo-/endoribonuclease and both RNase J and RNase E are involved in ribosomal RNA maturation. Mol Microbiol. 2011 Dec;82(5):1260-76. doi: 10.1111/j.1365-2958.2011.07888.x., Epub 2011 Nov 3. PMID:22014150 doi:http://dx.doi.org/10.1111/j.1365-2958.2011.07888.x
↑ Durand S, Gilet L, Bessieres P, Nicolas P, Condon C. Three essential ribonucleases-RNase Y, J1, and III-control the abundance of a majority of Bacillus subtilis mRNAs. PLoS Genet. 2012;8(3):e1002520. doi: 10.1371/journal.pgen.1002520. Epub 2012 Mar , 8. PMID:22412379 doi:http://dx.doi.org/10.1371/journal.pgen.1002520
↑ Figaro S, Durand S, Gilet L, Cayet N, Sachse M, Condon C. Bacillus subtilis mutants with knockouts of the genes encoding ribonucleases RNase Y and RNase J1 are viable, with major defects in cell morphology, sporulation, and competence. J Bacteriol. 2013 May;195(10):2340-8. doi: 10.1128/JB.00164-13. Epub 2013 Mar 15. PMID:23504012 doi:http://dx.doi.org/10.1128/JB.00164-13
↑ Newman JA, Hewitt L, Rodrigues C, Solovyova A, Harwood CR, Lewis RJ. Unusual, Dual Endo- and Exonuclease Activity in the Degradosome Explained by Crystal Structure Analysis of RNase J1. Structure. 2011 Sep 7;19(9):1241-51. PMID:21893285 doi:10.1016/j.str.2011.06.017

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3zq4"

@@ Line 3: / Line 3: @@
 <StructureSection load='3zq4' size='340' side='right'caption='[[3zq4]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3zq4]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacsu Bacsu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZQ4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ZQ4 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3zq4]] is a 4 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=3ZQ4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ZQ4 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=3zq4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zq4 OCA], [https://pdbe.org/3zq4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3zq4 RCSB], [https://www.ebi.ac.uk/pdbsum/3zq4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3zq4 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/RNJ1_BACSU RNJ1_BACSU]] An RNase that has endonuclease and 5'-3' exonuclease activity, playing a role in both rRNA and mRNA stability and degradation. Endonuclease activity can cleave within 4 nucleotides of the 5'-end of a triphosphorylated RNA. Endonuclease digestion by the RNase J1/J2 complex occurs at a different site and in some cases more efficiently than J1 or J2 alone. The exonuclease activity of the J1/J2 complex is highly processive on substrates longer than 5 nucleotides, on shorter substrates is distributive. Preferentially cleaves ssRNA, possibly in AU-rich regions. The 5'-exonuclease activity acts on 5'-hydroxyl and 5'-monophosphate but not 5'-triphosphate ends; it can digest through stem-loop structures if they are not too stable. Required for maturation of 16S rRNA. Acts preferentially on 16S rRNA precursors after association of the 30S and 50S ribosomal subunits. Plays a role in the secondary pathway of 23S rRNA 5' end maturation. Probably also participates in processing of pre-scRNA (the precursor of the signal recognition particle RNA).<ref>PMID:15831787</ref> <ref>PMID:17229210</ref> <ref>PMID:17512403</ref> <ref>PMID:17576666</ref> <ref>PMID:18204464</ref> <ref>PMID:18445592</ref> <ref>PMID:18713320</ref> <ref>PMID:19880604</ref> <ref>PMID:20025672</ref> <ref>PMID:21893286</ref> <ref>PMID:22014150</ref> <ref>PMID:22412379</ref> <ref>PMID:23504012</ref>
+[https://www.uniprot.org/uniprot/RNJ1_BACSU RNJ1_BACSU] An RNase that has endonuclease and 5'-3' exonuclease activity, playing a role in both rRNA and mRNA stability and degradation. Endonuclease activity can cleave within 4 nucleotides of the 5'-end of a triphosphorylated RNA. Endonuclease digestion by the RNase J1/J2 complex occurs at a different site and in some cases more efficiently than J1 or J2 alone. The exonuclease activity of the J1/J2 complex is highly processive on substrates longer than 5 nucleotides, on shorter substrates is distributive. Preferentially cleaves ssRNA, possibly in AU-rich regions. The 5'-exonuclease activity acts on 5'-hydroxyl and 5'-monophosphate but not 5'-triphosphate ends; it can digest through stem-loop structures if they are not too stable. Required for maturation of 16S rRNA. Acts preferentially on 16S rRNA precursors after association of the 30S and 50S ribosomal subunits. Plays a role in the secondary pathway of 23S rRNA 5' end maturation. Probably also participates in processing of pre-scRNA (the precursor of the signal recognition particle RNA).<ref>PMID:15831787</ref> <ref>PMID:17229210</ref> <ref>PMID:17512403</ref> <ref>PMID:17576666</ref> <ref>PMID:18204464</ref> <ref>PMID:18445592</ref> <ref>PMID:18713320</ref> <ref>PMID:19880604</ref> <ref>PMID:20025672</ref> <ref>PMID:21893286</ref> <ref>PMID:22014150</ref> <ref>PMID:22412379</ref> <ref>PMID:23504012</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 25: / Line 26: @@
 __TOC__
 </StructureSection>
-[[Category: Bacsu]]
+[[Category: Bacillus subtilis subsp. subtilis str. 168]]
 [[Category: Large Structures]]
-[[Category: Harwood, C R]]
+[[Category: Harwood CR]]
-[[Category: Hewitt, L]]
+[[Category: Hewitt L]]
-[[Category: Lewis, R J]]
+[[Category: Lewis RJ]]
-[[Category: Newman, J A]]
+[[Category: Newman JA]]
-[[Category: Rodrigues, C]]
+[[Category: Rodrigues C]]
-[[Category: Solovyova, A]]
+[[Category: Solovyova A]]
-[[Category: Hydrolase]]
-[[Category: Rna maturation]]

3zq4

From Proteopedia

Current revision

Unusual, dual endo- and exo-nuclease activity in the degradosome explained by crystal structure analysis of RNase J1

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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