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4tm6

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Crystal Structure of EutL from Clostridium Perfringens at 298K

Structural highlights

4tm6 is a 3 chain structure with sequence from Clostridium perfringens E str. JGS1987. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.9002Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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).^[1] ^[2] ^[3] ^[4] ^[5]

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^[6]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Thompson MC, Crowley CS, Kopstein J, Bobik TA, Yeates TO. Structure of a bacterial microcompartment shell protein bound to a cobalamin cofactor. Acta Crystallogr F Struct Biol Commun. 2014 Dec 1;70(Pt 12):1584-90. doi:, 10.1107/S2053230X1402158X. Epub 2014 Nov 14. PMID:25484204 doi:http://dx.doi.org/10.1107/S2053230X1402158X
↑ Thompson MC, Cascio D, Leibly DJ, Yeates TO. An allosteric model for control of pore opening by substrate binding in the eutl microcompartment shell protein. Protein Sci. 2015 Mar 9. doi: 10.1002/pro.2672. PMID:25752492 doi:http://dx.doi.org/10.1002/pro.2672
↑ Thompson MC, Crowley CS, Kopstein J, Bobik TA, Yeates TO. Structure of a bacterial microcompartment shell protein bound to a cobalamin cofactor. Acta Crystallogr F Struct Biol Commun. 2014 Dec 1;70(Pt 12):1584-90. doi:, 10.1107/S2053230X1402158X. Epub 2014 Nov 14. PMID:25484204 doi:http://dx.doi.org/10.1107/S2053230X1402158X
↑ Thompson MC, Cascio D, Leibly DJ, Yeates TO. An allosteric model for control of pore opening by substrate binding in the eutl microcompartment shell protein. Protein Sci. 2015 Mar 9. doi: 10.1002/pro.2672. PMID:25752492 doi:http://dx.doi.org/10.1002/pro.2672
↑ Thompson MC, Cascio D, Yeates TO. Microfocus diffraction from different regions of a protein crystal: structural variations and unit-cell polymorphism. Acta Crystallogr D Struct Biol. 2018 May 1;74(Pt 5):411-421. doi:, 10.1107/S2059798318003479. Epub 2018 Apr 24. PMID:29717712 doi:http://dx.doi.org/10.1107/S2059798318003479
↑ Thompson MC, Cascio D, Leibly DJ, Yeates TO. An allosteric model for control of pore opening by substrate binding in the eutl microcompartment shell protein. Protein Sci. 2015 Mar 9. doi: 10.1002/pro.2672. PMID:25752492 doi:http://dx.doi.org/10.1002/pro.2672

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4tm6"

Categories: Clostridium perfringens E str. JGS1987 | Large Structures | Cascio D | Thompson MC | Yeates TO

@@ Line 4: / Line 4: @@
 == Structural highlights ==
 <table><tr><td colspan='2'>[[4tm6]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Clostridium_perfringens_E_str._JGS1987 Clostridium perfringens E str. JGS1987]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4TM6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4TM6 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]] 1.9002&#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=4tm6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4tm6 OCA], [https://pdbe.org/4tm6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4tm6 RCSB], [https://www.ebi.ac.uk/pdbsum/4tm6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4tm6 ProSAT]</span></td></tr>
 </table>

4tm6

From Proteopedia

Current revision

Crystal Structure of EutL from Clostridium Perfringens at 298K

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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