6a4d: Difference between revisions

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<StructureSection load='6a4d' size='340' side='right'caption='[[6a4d]], [[Resolution|resolution]] 2.19&Aring;' scene=''>
<StructureSection load='6a4d' size='340' side='right'caption='[[6a4d]], [[Resolution|resolution]] 2.19&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[6a4d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6A4D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6A4D FirstGlance]. <br>
<table><tr><td colspan='2'>[[6a4d]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Colwellia_psychrerythraea_34H Colwellia psychrerythraea 34H]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6A4D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6A4D FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=9RC:5-O-[(S)-hydroxy(4-nitrophenoxy)phosphoryl]thymidine'>9RC</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]] 2.19&#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=6a4d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6a4d OCA], [http://pdbe.org/6a4d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6a4d RCSB], [http://www.ebi.ac.uk/pdbsum/6a4d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6a4d ProSAT]</span></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=9RC:5-O-[(S)-hydroxy(4-nitrophenoxy)phosphoryl]thymidine'>9RC</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=6a4d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6a4d OCA], [https://pdbe.org/6a4d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6a4d RCSB], [https://www.ebi.ac.uk/pdbsum/6a4d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6a4d ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/ORN_COLP3 ORN_COLP3]] 3'-to-5' exoribonuclease specific for small oligoribonucleotides.
[https://www.uniprot.org/uniprot/ORN_COLP3 ORN_COLP3] 3'-to-5' exoribonuclease specific for small oligoribonucleotides.
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Cells regulate their intracellular mRNA levels by using specific ribonucleases. Oligoribonuclease (ORN) is a 3'-5' exoribonuclease for small RNA molecules, important in RNA degradation and re-utilisation. However, there is no structural information on the ligand-binding form of ORNs. In this study, the crystal structures of oligoribonuclease from Colwellia psychrerythraea strain 34H (CpsORN) were determined in four different forms: unliganded-structure, thymidine 5'-monophosphate p-nitrophenyl ester (pNP-TMP)-bound, two separated uridine-bound, and two linked uridine (U-U)-bound forms. The crystal structures show that CpsORN is a tight dimer, with two separated active sites and one divalent metal cation ion in each active site. These structures represent several snapshots of the enzymatic reaction process, which allowed us to suggest a possible one-metal-dependent reaction mechanism for CpsORN. Moreover, the biochemical data support our suggested mechanism and identified the key residues responsible for enzymatic catalysis of CpsORN.


Structural basis of small RNA hydrolysis by oligoribonuclease (CpsORN) from Colwellia psychrerythraea strain 34H.,Lee CW, Park SH, Jeong CS, Cha SS, Park H, Lee JH Sci Rep. 2019 Feb 25;9(1):2649. doi: 10.1038/s41598-019-39641-0. PMID:30804410<ref>PMID:30804410</ref>
==See Also==
 
*[[Exonuclease 3D structures|Exonuclease 3D structures]]
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
</div>
<div class="pdbe-citations 6a4d" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Colwellia psychrerythraea 34H]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Lee, C W]]
[[Category: Lee CW]]
[[Category: Lee, J H]]
[[Category: Lee JH]]
[[Category: Park, S]]
[[Category: Park S]]
[[Category: Colwellia psychrerythraea strain 34h]]
[[Category: Exonuclease]]
[[Category: Hydrolase]]
[[Category: Oligoribonuclease]]

Latest revision as of 10:30, 27 March 2024

pNP-TMP bound Oligoribonuclease (ORN) from Colwellia psychrerythraea strain 34H

6a4d, resolution 2.19Å

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