4ts9: Difference between revisions
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==Crystal structure of wild type E. Coli purine nucleoside phosphorylase with 6 FMC molecules== | ==Crystal structure of wild type E. Coli purine nucleoside phosphorylase with 6 FMC molecules== | ||
<StructureSection load='4ts9' size='340' side='right' caption='[[4ts9]], [[Resolution|resolution]] 1.77Å' scene=''> | <StructureSection load='4ts9' size='340' side='right'caption='[[4ts9]], [[Resolution|resolution]] 1.77Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[4ts9]] is a 3 chain structure with sequence from [ | <table><tr><td colspan='2'>[[4ts9]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4TS9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4TS9 FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMC:(1S)-1-(7-AMINO-1H-PYRAZOLO[4,3-D]PYRIMIDIN-3-YL)-1,4-ANHYDRO-D-RIBITOL'>FMC</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.77Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMC:(1S)-1-(7-AMINO-1H-PYRAZOLO[4,3-D]PYRIMIDIN-3-YL)-1,4-ANHYDRO-D-RIBITOL'>FMC</scene>, <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'>[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4ts9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ts9 OCA], [https://pdbe.org/4ts9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ts9 RCSB], [https://www.ebi.ac.uk/pdbsum/4ts9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ts9 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/DEOD_ECOLI DEOD_ECOLI] Cleavage of guanosine or inosine to respective bases and sugar-1-phosphate molecules.[HAMAP-Rule:MF_01627] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Purine nucleoside phosphorylase (PNP) catalyses the cleavage of the glycosidic bond of purine nucleosides using phosphate instead of water as a second substrate. PNP from Escherichia coli is a homohexamer, build as a trimer of dimers, and each subunit can be in two conformations, open or closed. This conformational change is induced by the presence of phosphate substrate, and very likely a required step for the catalysis. Closing one active site strongly affects the others, by a yet unclear mechanism and order of events. Kinetic and ligand binding studies show strong negative cooperativity between subunits. Here, for the first time, we managed to monitor the sequence of nucleoside binding to individual subunits in the crystal structures of the wild-type enzyme, showing that first the closed sites, not the open ones, are occupied by the nucleoside. However, two mutations within the active site, Asp204Ala/Arg217Ala, are enough not only to significantly reduce the effectiveness of the enzyme, but also reverse the sequence of the nucleoside binding. In the mutant the open sites, neighbours in a dimer of those in the closed conformation, are occupied as first. This demonstrates how important for the effective catalysis of Escherichia coli PNP is proper subunit cooperation. | |||
Crystallographic snapshots of ligand binding to hexameric purine nucleoside phosphorylase and kinetic studies give insight into the mechanism of catalysis.,Stefanic Z, Narczyk M, Mikleusevic G, Kazazic S, Bzowska A, Luic M Sci Rep. 2018 Oct 18;8(1):15427. doi: 10.1038/s41598-018-33723-1. PMID:30337572<ref>PMID:30337572</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 4ts9" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Purine nucleoside phosphorylase 3D structures|Purine nucleoside phosphorylase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Escherichia coli]] | [[Category: Escherichia coli]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: | [[Category: Bzowska A]] | ||
[[Category: | [[Category: Stefanic Z]] | ||