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| | ==Crystal Structure of E. coli polynucleotide phosphorylase bound to RNA and RNase E== | | ==Crystal Structure of E. coli polynucleotide phosphorylase bound to RNA and RNase E== |
| - | <StructureSection load='3gcm' size='340' side='right' caption='[[3gcm]], [[Resolution|resolution]] 2.50Å' scene=''> | + | <StructureSection load='3gcm' size='340' side='right'caption='[[3gcm]], [[Resolution|resolution]] 2.50Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3gcm]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_e24377a Escherichia coli e24377a]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GCM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GCM FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3gcm]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] and [https://en.wikipedia.org/wiki/Escherichia_coli_O139:H28_str._E24377A Escherichia coli O139:H28 str. E24377A]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GCM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GCM FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5GP:GUANOSINE-5-MONOPHOSPHATE'>5GP</scene>, <scene name='pdbligand=FLC:CITRATE+ANION'>FLC</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 2.5Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3gll|3gll]], [[3gme|3gme]]</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5GP:GUANOSINE-5-MONOPHOSPHATE'>5GP</scene>, <scene name='pdbligand=FLC:CITRATE+ANION'>FLC</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Polyribonucleotide_nucleotidyltransferase Polyribonucleotide nucleotidyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.8 2.7.7.8] </span></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=3gcm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gcm OCA], [https://pdbe.org/3gcm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3gcm RCSB], [https://www.ebi.ac.uk/pdbsum/3gcm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3gcm 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=3gcm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gcm OCA], [http://pdbe.org/3gcm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3gcm RCSB], [http://www.ebi.ac.uk/pdbsum/3gcm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3gcm ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/PNP_ECO24 PNP_ECO24]] Involved in mRNA degradation. Hydrolyzes single-stranded polyribonucleotides processively in the 3'- to 5'-direction (By similarity). | + | [https://www.uniprot.org/uniprot/PNP_ECO24 PNP_ECO24] Involved in mRNA degradation. Hydrolyzes single-stranded polyribonucleotides processively in the 3'- to 5'-direction (By similarity). |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | ==See Also== | | ==See Also== |
| - | *[[Ribonuclease|Ribonuclease]] | + | *[[Ribonuclease 3D structures|Ribonuclease 3D structures]] |
| - | *[[Temp|Temp]]
| + | |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Escherichia coli e24377a]] | + | [[Category: Escherichia coli]] |
| - | [[Category: Polyribonucleotide nucleotidyltransferase]] | + | [[Category: Escherichia coli O139:H28 str. E24377A]] |
| - | [[Category: Luisi, B L]]
| + | [[Category: Large Structures]] |
| - | [[Category: Nurmohamed, S]] | + | [[Category: Luisi BL]] |
| - | [[Category: Cytoplasm]] | + | [[Category: Nurmohamed S]] |
| - | [[Category: Hydrolase]] | + | |
| - | [[Category: Nucleotidyltransferase]]
| + | |
| - | [[Category: Protein-rna complex]]
| + | |
| - | [[Category: Rna-binding]]
| + | |
| - | [[Category: Transferase]]
| + | |
| - | [[Category: Transferase - protein binding complex]]
| + | |
| Structural highlights
Function
PNP_ECO24 Involved in mRNA degradation. Hydrolyzes single-stranded polyribonucleotides processively in the 3'- to 5'-direction (By similarity).
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
Polynucleotide phosphorylase (PNPase) is a processive exoribonuclease that contributes to messenger RNA turnover and quality control of ribosomal RNA precursors in many bacterial species. In Escherichia coli, a proportion of the PNPase is recruited into a multi-enzyme assembly, known as the RNA degradosome, through an interaction with the scaffolding domain of the endoribonuclease RNase E. Here, we report crystal structures of E. coli PNPase complexed with the recognition site from RNase E and with manganese in the presence or in the absence of modified RNA. The homotrimeric PNPase engages RNase E on the periphery of its ring-like architecture through a pseudo-continuous anti-parallel beta-sheet. A similar interaction pattern occurs in the structurally homologous human exosome between the Rrp45 and Rrp46 subunits. At the centre of the PNPase ring is a tapered channel with an adjustable aperture where RNA bases stack on phenylalanine side chains and trigger structural changes that propagate to the active sites. Manganese can substitute for magnesium as an essential co-factor for PNPase catalysis, and our crystal structure of the enzyme in complex with manganese suggests how the metal is positioned to stabilise the transition state. We discuss the implications of these structural observations for the catalytic mechanism of PNPase, its processive mode of action, and its assembly into the RNA degradosome.
Crystal structure of Escherichia coli polynucleotide phosphorylase core bound to RNase E, RNA and manganese: implications for catalytic mechanism and RNA degradosome assembly.,Nurmohamed S, Vaidialingam B, Callaghan AJ, Luisi BF J Mol Biol. 2009 May 29;389(1):17-33. Epub 2009 Mar 24. PMID:19327365[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Nurmohamed S, Vaidialingam B, Callaghan AJ, Luisi BF. Crystal structure of Escherichia coli polynucleotide phosphorylase core bound to RNase E, RNA and manganese: implications for catalytic mechanism and RNA degradosome assembly. J Mol Biol. 2009 May 29;389(1):17-33. Epub 2009 Mar 24. PMID:19327365 doi:10.1016/j.jmb.2009.03.051
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