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4xwt

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Revision as of 17:55, 26 April 2023

Crystal structure of RNase J complexed with UMP

Structural highlights

4xwt is a 2 chain structure with sequence from Deinococcus radiodurans. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

H9CZL7_DEIRD

Publication Abstract from PubMed

RNase J is a conserved ribonuclease that belongs to the beta-CASP family of nucleases. It possesses both endo- and exo-ribonuclease activities, which play a key role in pre-rRNA maturation and mRNA decay. Here we report high-resolution crystal structures of Deinococcus radiodurans RNase J complexed with RNA or uridine 5'-monophosphate in the presence of manganese ions. Biochemical and structural studies revealed that RNase J uses zinc ions for two-metal-ion catalysis. One residue conserved among RNase J orthologues (motif B) forms specific electrostatic interactions with the scissile phosphate of the RNA that is critical for the catalysis and product stabilization. The additional manganese ion, which is coordinated by conserved residues at the dimer interface, is critical for RNase J dimerization and exonuclease activity. The structures may also shed light on the mechanism of RNase J exo- and endonucleolytic activity switch.

Structural insights into catalysis and dimerization enhanced exonuclease activity of RNase J.,Zhao Y, Lu M, Zhang H, Hu J, Zhou C, Xu Q, Ul Hussain Shah AM, Xu H, Wang L, Hua Y Nucleic Acids Res. 2015 Jun 23;43(11):5550-9. doi: 10.1093/nar/gkv444. Epub 2015 , May 4. PMID:25940620^[1]

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

References

↑ Zhao Y, Lu M, Zhang H, Hu J, Zhou C, Xu Q, Ul Hussain Shah AM, Xu H, Wang L, Hua Y. Structural insights into catalysis and dimerization enhanced exonuclease activity of RNase J. Nucleic Acids Res. 2015 Jun 23;43(11):5550-9. doi: 10.1093/nar/gkv444. Epub 2015 , May 4. PMID:25940620 doi:http://dx.doi.org/10.1093/nar/gkv444

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/4xwt"

@@ Line 3: / Line 3: @@
 <StructureSection load='4xwt' size='340' side='right'caption='[[4xwt]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4xwt]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"micrococcus_radiodurans"_raj_et_al._1960 "micrococcus radiodurans" raj et al. 1960]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XWT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XWT FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4xwt]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Deinococcus_radiodurans Deinococcus radiodurans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XWT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XWT FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=U5P:URIDINE-5-MONOPHOSPHATE'>U5P</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=U5P:URIDINE-5-MONOPHOSPHATE'>U5P</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4xww|4xww]]</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=4xwt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xwt OCA], [https://pdbe.org/4xwt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xwt RCSB], [https://www.ebi.ac.uk/pdbsum/4xwt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xwt ProSAT]</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=4xwt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xwt OCA], [http://pdbe.org/4xwt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xwt RCSB], [http://www.ebi.ac.uk/pdbsum/4xwt PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4xwt ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/H9CZL7_DEIRD H9CZL7_DEIRD]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 19: / Line 20: @@
 ==See Also==
-*[[Ribonuclease|Ribonuclease]]
+*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Micrococcus radiodurans raj et al. 1960]]
+[[Category: Deinococcus radiodurans]]
 [[Category: Large Structures]]
-[[Category: Hua, Y]]
+[[Category: Hua Y]]
-[[Category: Lu, M]]
+[[Category: Lu M]]
-[[Category: Xu, Q]]
+[[Category: Xu Q]]
-[[Category: Zhang, H]]
+[[Category: Zhang H]]
-[[Category: Zhao, Y]]
+[[Category: Zhao Y]]
-[[Category: Deinococcus radioduran]]
-[[Category: Dimerization]]
-[[Category: Manganese]]
-[[Category: Ribonuclease]]
-[[Category: Rna binding protein]]
-[[Category: Two-metal-ion]]

4xwt

From Proteopedia

Revision as of 17:55, 26 April 2023

Crystal structure of RNase J complexed with UMP

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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