4am3: Difference between revisions
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==Crystal structure of C. crescentus PNPase bound to RNA== | ==Crystal structure of C. crescentus PNPase bound to RNA== | ||
<StructureSection load='4am3' size='340' side='right' caption='[[4am3]], [[Resolution|resolution]] 3.00Å' scene=''> | <StructureSection load='4am3' size='340' side='right'caption='[[4am3]], [[Resolution|resolution]] 3.00Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[4am3]] is a 7 chain structure with sequence from [ | <table><tr><td colspan='2'>[[4am3]] is a 7 chain structure with sequence from [https://en.wikipedia.org/wiki/Caulobacter_vibrioides_CB15 Caulobacter vibrioides CB15] and [https://en.wikipedia.org/wiki/Escherichia_coli_BL21(DE3) Escherichia coli BL21(DE3)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4AM3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4AM3 FirstGlance]. <br> | ||
</td></tr><tr id=' | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3Å</td></tr> | ||
<tr id=' | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=4am3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4am3 OCA], [https://pdbe.org/4am3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4am3 RCSB], [https://www.ebi.ac.uk/pdbsum/4am3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4am3 ProSAT]</span></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | |||
</table> | </table> | ||
== Function == | == Function == | ||
[ | [https://www.uniprot.org/uniprot/PNP_CAUVC PNP_CAUVC] Involved in mRNA degradation. Catalyzes the phosphorolysis of single-stranded polyribonucleotides processively in the 3'- to 5'-direction.[HAMAP-Rule:MF_01595] | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
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</div> | </div> | ||
<div class="pdbe-citations 4am3" style="background-color:#fffaf0;"></div> | <div class="pdbe-citations 4am3" style="background-color:#fffaf0;"></div> | ||
==See Also== | |||
*[[Ribonuclease 3D structures|Ribonuclease 3D structures]] | |||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Caulobacter vibrioides CB15]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: Gubbey T]] | |||
[[Category: Gubbey | [[Category: Hardwick SW]] | ||
[[Category: Hardwick | [[Category: Hug I]] | ||
[[Category: Hug | [[Category: Jenal U]] | ||
[[Category: Jenal | [[Category: Luisi BF]] | ||
[[Category: Luisi | |||
Latest revision as of 14:29, 20 December 2023
Crystal structure of C. crescentus PNPase bound to RNACrystal structure of C. crescentus PNPase bound to RNA
Structural highlights
FunctionPNP_CAUVC Involved in mRNA degradation. Catalyzes the phosphorolysis of single-stranded polyribonucleotides processively in the 3'- to 5'-direction.[HAMAP-Rule:MF_01595] Publication Abstract from PubMedPolynucleotide phosphorylase (PNPase) is an exoribonuclease that cleaves single-stranded RNA substrates with 3'-5' directionality and processive behaviour. Its ring-like, trimeric architecture creates a central channel where phosphorolytic active sites reside. One face of the ring is decorated with RNA-binding K-homology (KH) and S1 domains, but exactly how these domains help to direct the 3' end of single-stranded RNA substrates towards the active sites is an unsolved puzzle. Insight into this process is provided by our crystal structures of RNA-bound and apo Caulobacter crescentus PNPase. In the RNA-free form, the S1 domains adopt a 'splayed' conformation that may facilitate capture of RNA substrates. In the RNA-bound structure, the three KH domains collectively close upon the RNA and direct the 3' end towards a constricted aperture at the entrance of the central channel. The KH domains make non-equivalent interactions with the RNA, and there is a marked asymmetry within the catalytic core of the enzyme. On the basis of these data, we propose that structural non-equivalence, induced upon RNA binding, helps to channel substrate to the active sites through mechanical ratcheting. Structural and biochemical analyses also reveal the basis for PNPase association with RNase E in the multi-enzyme RNA degradosome assembly of the alpha-proteobacteria. Crystal structure of Caulobacter crescentus polynucleotide phosphorylase reveals a mechanism of RNA substrate channelling and RNA degradosome assembly.,Hardwick SW, Gubbey T, Hug I, Jenal U, Luisi BF Open Biol. 2012 Apr;2(4):120028. PMID:22724061[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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