4fdz: Difference between revisions

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== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[4fdz]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Clostridium_perfringens Clostridium perfringens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FDZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4FDZ FirstGlance]. <br>
<table><tr><td colspan='2'>[[4fdz]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Clostridium_perfringens Clostridium perfringens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FDZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4FDZ FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 1.802&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</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=4fdz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fdz OCA], [https://pdbe.org/4fdz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4fdz RCSB], [https://www.ebi.ac.uk/pdbsum/4fdz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4fdz ProSAT]</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=4fdz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fdz OCA], [https://pdbe.org/4fdz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4fdz RCSB], [https://www.ebi.ac.uk/pdbsum/4fdz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4fdz ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[https://www.uniprot.org/uniprot/EUTL_CLOPE EUTL_CLOPE] A component of the bacterial microcompartment (BMC) shell dedicated to ethanolamine degradation. May be involved in cofactor diffusion across the BMC (Probable). Cobalamin is covalently bound to 1 subunit of the trimer on the concave (lumenal) face in a closed pore conformation; whether this is physiologically relevant is unclear (PubMed:25484204). The closed form has 3 very narrow channels (1.3 Angstrom at their narrowest) per trimer lined by acidic and aromatic residues; 2 ethanolamine molecules can bind in each channel, on either side of the constriction. Does not bind acetate, ethanol or acetyl phosphate, all of which are small molecules involved in ethanolamine metabolism (PubMed:25752492). Ethanolamine-binding has been hypothesized to stabilize the EutL central pore in a closed (non-transporting) state. An open pore is thought to be large enough to transport ATP and/or cobalamin (Probable).<ref>PMID:25484204</ref> <ref>PMID:25752492</ref> <ref>PMID:25484204</ref> <ref>PMID:25752492</ref> <ref>PMID:29717712</ref>  
[https://www.uniprot.org/uniprot/EUTL_CLOPE EUTL_CLOPE] A component of the bacterial microcompartment (BMC) shell dedicated to ethanolamine degradation. May be involved in cofactor diffusion across the BMC (Probable). Cobalamin is covalently bound to 1 subunit of the trimer on the concave (lumenal) face in a closed pore conformation; whether this is physiologically relevant is unclear (PubMed:25484204). The closed form has 3 very narrow channels (1.3 Angstrom at their narrowest) per trimer lined by acidic and aromatic residues; 2 ethanolamine molecules can bind in each channel, on either side of the constriction. Does not bind acetate, ethanol or acetyl phosphate, all of which are small molecules involved in ethanolamine metabolism (PubMed:25752492). Ethanolamine-binding has been hypothesized to stabilize the EutL central pore in a closed (non-transporting) state. An open pore is thought to be large enough to transport ATP and/or cobalamin (Probable).<ref>PMID:25484204</ref> <ref>PMID:25752492</ref> <ref>PMID:25484204</ref> <ref>PMID:25752492</ref> <ref>PMID:29717712</ref>  
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The ethanolamine utilization (Eut) microcompartment is a protein-based metabolic organelle that is strongly associated with pathogenesis in bacteria that inhabit the human gut. The exterior shell of this elaborate protein complex is composed from a few thousand copies of BMC-domain shell proteins, which form a semi-permeable diffusion barrier that provides the interior enzymes with substrates and cofactors while simultaneously retaining metabolic intermediates. The ability of this protein shell to regulate passage of substrate and cofactor molecules is critical for microcompartment function, but the details of how this diffusion barrier can allow the passage of large cofactors while still retaining small intermediates remain unclear. Previous work has revealed two conformations of the EutL shell protein, providing substantial evidence for a gated pore that might allow the passage of large cofactors. Here we report structural and biophysical evidence to show that ethanolamine, the substrate of the Eut microcompartment, acts as a negative allosteric regulator of EutL pore opening. Specifically, a series of X-ray crystal structures of EutL from Clostridium perfringens, along with equilibrium binding studies, reveal that ethanolamine binds to EutL at a site that exists in the closed-pore conformation and which is incompatible with opening of the large pore for cofactor transport. The allosteric mechanism we propose is consistent with the cofactor requirements of the Eut microcompartment, leading to a new model for EutL function. Furthermore, our results suggest the possibility of redox modulation of the allosteric mechanism, opening potentially new lines of investigation. This article is protected by copyright. All rights reserved.
An allosteric model for control of pore opening by substrate binding in the eutl microcompartment shell protein.,Thompson MC, Cascio D, Leibly DJ, Yeates TO Protein Sci. 2015 Mar 9. doi: 10.1002/pro.2672. PMID:25752492<ref>PMID:25752492</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 4fdz" style="background-color:#fffaf0;"></div>
== References ==
== References ==
<references/>
<references/>

Latest revision as of 15:22, 14 March 2024

EutL from Clostridium perfringens, Crystallized Under Reducing Conditions

4fdz, resolution 1.80Å

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