View source for 5y48


==Crystal structure of the complex of Ribosome inactivating protein from Momordica balsamina with Pyrimidine-2,4-dione at 1.70 Angstrom resolution==
<StructureSection load='5y48' size='340' side='right'caption='[[5y48]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5y48]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Momordica_balsamina Momordica balsamina]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y48 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5Y48 FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.7&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=URA:URACIL'>URA</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=5y48 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y48 OCA], [https://pdbe.org/5y48 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5y48 RCSB], [https://www.ebi.ac.uk/pdbsum/5y48 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5y48 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/D9J2T9_MOMBA D9J2T9_MOMBA] 
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Ribosome inactivating protein (RIP) catalyzes the cleavage of glycosidic bond formed between adenine and ribose sugar of ribosomal RNA to inactivate ribosomes. Previous structural studies have shown that RNA bases, adenine, guanine, and cytosine tend to bind to RIP in the substrate binding site. However, the mode of binding of uracil with RIP was not yet known. Here, we report crystal structures of two complexes of type 1 RIP from Momordica balsamina (MbRIP1) with base, uracil and nucleoside, uridine. The binding studies of MbRIP1 with uracil and uridine as estimated using fluorescence spectroscopy showed that the equilibrium dissociation constants (KD ) were 1.2 x 10(-6) M and 1.4 x 10(-7) M respectively. The corresponding values obtained using surface plasmon resonance (SPR) were found to be 1.4 x 10(-6) M and 1.1 x 10(-7) M, respectively. Structures of the complexes of MbRIP1 with uracil (Structure-1) and uridine (Structure-2) were determined at 1.70 and 1.98 A resolutions respectively. Structure-1 showed that uracil bound to MbRIP1 at the substrate binding site but its mode of binding was significantly different from those of adenine, guanine and cytosine. However, the mode of binding of uridine was found to be similar to those of cytidine. As a result of binding of uracil to MbRIP1 at the substrate binding site, three water molecules were expelled while eight water molecules were expelled when uridine bound to MbRIP1.

Binding and structural studies of the complexes of type 1 ribosome inactivating protein from Momordica balsamina with uracil and uridine.,Pandey SN, Iqbal N, Singh PK, Rastogi N, Kaur P, Sharma S, Singh TP Proteins. 2019 Feb;87(2):99-109. doi: 10.1002/prot.25584. Epub 2018 Nov 5. PMID:30007053<ref>PMID:30007053</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5y48" style="background-color:#fffaf0;"></div>

==See Also==
*[[Ribosome inactivating protein 3D structures|Ribosome inactivating protein 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Momordica balsamina]]
[[Category: Iqbal N]]
[[Category: Kaur P]]
[[Category: Pandey S]]
[[Category: Sharma S]]
[[Category: Singh PK]]
[[Category: Singh TP]]