5a0t: Difference between revisions
New page: '''Unreleased structure''' The entry 5a0t is ON HOLD Authors: Pei, X.Y., Bralley, P., Jones, G.H., Luisi, B.F. Description: Catalysis and 5' end sensing by ribonuclease RNase J of the ... |
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==Catalysis and 5' end sensing by ribonuclease RNase J of the metallo- beta-lactamase family== | |||
<StructureSection load='5a0t' size='340' side='right'caption='[[5a0t]], [[Resolution|resolution]] 2.28Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[5a0t]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_BL21(DE3) Escherichia coli BL21(DE3)] and [https://en.wikipedia.org/wiki/Streptomyces_coelicolor_A3(2) Streptomyces coelicolor A3(2)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5A0T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5A0T FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.283Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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=5a0t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5a0t OCA], [https://pdbe.org/5a0t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5a0t RCSB], [https://www.ebi.ac.uk/pdbsum/5a0t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5a0t ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/O86842_STRCO O86842_STRCO] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
In diverse bacterial species, the turnover and processing of many RNAs is mediated by the ribonuclease RNase J, a member of the widely occurring metallo-beta-lactamase enzyme family. We present crystal structures of Streptomyces coelicolor RNase J with bound RNA in pre- and post-cleavage states, at 2.27 A and 2.80 A resolution, respectively. These structures reveal snapshots of the enzyme cleaving substrate directionally and sequentially from the 5' terminus. In the pre-cleavage state, a water molecule is coordinated to a zinc ion pair in the active site but is imperfectly oriented to launch a nucleophilic attack on the phosphate backbone. A conformational switch is envisaged that enables the in-line positioning of the attacking water and may be facilitated by magnesium ions. Adjacent to the scissile bond, four bases are stacked in a tightly sandwiching pocket, and mutagenesis results indicate that this organization helps to drive processive exo-ribonucleolytic cleavage. Like its numerous homologues, S. coelicolor RNase J can also cleave some RNA internally, and the structural data suggest how the preference for exo- versus endo-cleavage mode is linked with recognition of the chemical status of the substrate's 5' end. | |||
Linkage of catalysis and 5' end recognition in ribonuclease RNase J.,Pei XY, Bralley P, Jones GH, Luisi BF Nucleic Acids Res. 2015 Aug 7. pii: gkv732. PMID:26253740<ref>PMID:26253740</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: | <div class="pdbe-citations 5a0t" style="background-color:#fffaf0;"></div> | ||
[[Category: | |||
[[Category: | ==See Also== | ||
[[Category: | *[[Ribonuclease 3D structures|Ribonuclease 3D structures]] | ||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Bralley P]] | |||
[[Category: Jones GH]] | |||
[[Category: Luisi BF]] | |||
[[Category: Pei XY]] | |||
Latest revision as of 14:02, 10 January 2024
Catalysis and 5' end sensing by ribonuclease RNase J of the metallo- beta-lactamase familyCatalysis and 5' end sensing by ribonuclease RNase J of the metallo- beta-lactamase family
Structural highlights
FunctionPublication Abstract from PubMedIn diverse bacterial species, the turnover and processing of many RNAs is mediated by the ribonuclease RNase J, a member of the widely occurring metallo-beta-lactamase enzyme family. We present crystal structures of Streptomyces coelicolor RNase J with bound RNA in pre- and post-cleavage states, at 2.27 A and 2.80 A resolution, respectively. These structures reveal snapshots of the enzyme cleaving substrate directionally and sequentially from the 5' terminus. In the pre-cleavage state, a water molecule is coordinated to a zinc ion pair in the active site but is imperfectly oriented to launch a nucleophilic attack on the phosphate backbone. A conformational switch is envisaged that enables the in-line positioning of the attacking water and may be facilitated by magnesium ions. Adjacent to the scissile bond, four bases are stacked in a tightly sandwiching pocket, and mutagenesis results indicate that this organization helps to drive processive exo-ribonucleolytic cleavage. Like its numerous homologues, S. coelicolor RNase J can also cleave some RNA internally, and the structural data suggest how the preference for exo- versus endo-cleavage mode is linked with recognition of the chemical status of the substrate's 5' end. Linkage of catalysis and 5' end recognition in ribonuclease RNase J.,Pei XY, Bralley P, Jones GH, Luisi BF Nucleic Acids Res. 2015 Aug 7. pii: gkv732. PMID:26253740[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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