View source for 5vp3


==Light-sensitive photoprotein==
<StructureSection load='5vp3' size='340' side='right'caption='[[5vp3]], [[Resolution|resolution]] 2.15&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5vp3]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mnemiopsis_leidyi Mnemiopsis leidyi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VP3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5VP3 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]] 2.151&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=SCN:THIOCYANATE+ION'>SCN</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=5vp3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vp3 OCA], [https://pdbe.org/5vp3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5vp3 RCSB], [https://www.ebi.ac.uk/pdbsum/5vp3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5vp3 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/E0WVU4_MNELE E0WVU4_MNELE] 
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Bioluminescence of a variety of marine organisms, mostly cnidarians and ctenophores, is carried out by Ca(2+)-dependent photoproteins. The mechanism of light emission operates via the same reaction in both animal families. Despite numerous studies on the ctenophore photoprotein family, the detailed catalytic mechanism and arrangement of amino acid residues surrounding the chromophore in this family are a mystery. Here, we report the crystal structure of Cd(2+)-loaded apo-mnemiopsin1, a member of the ctenophore family, at 2.15 A resolution and used quantum mechanics/molecular mechanics (QM/MM) to investigate its reaction mechanism. The simulations suggested that an Asp-156-Arg-39-Tyr-202 triad creates a hydrogen-bonded network to facilitate the transfer of a proton from the 2-hydroperoxy group of the chromophore coelenterazine to bulk solvent. We identified a water molecule in the coelenteramide-binding cavity that forms a hydrogen bond with the amide nitrogen atom of coelenteramide, which, in turn, is hydrogen-bonded via another water molecule to Tyr-131. This observation supports the hypothesis that the function of the coelenteramide-bound water molecule is to catalyze the 2-hydroperoxycoelenterazine decarboxylation reaction by protonation of a dioxetanone anion, thereby triggering the bioluminescence reaction in the ctenophore photoprotein family.

Reaction mechanism of the bioluminescent protein mnemiopsin1 revealed by X-ray crystallography and QM/MM simulations.,Molakarimi M, Gorman MA, Mohseni A, Pashandi Z, Taghdir M, Naderi-Manesh H, Sajedi RH, Parker MW J Biol Chem. 2019 Jan 4;294(1):20-27. doi: 10.1074/jbc.RA118.006053. Epub 2018, Nov 12. PMID:30420427<ref>PMID:30420427</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5vp3" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Mnemiopsis leidyi]]
[[Category: Gorman MA]]
[[Category: Parker MW]]