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| | ==Crystal Structure of the EutL Microcompartment Shell Protein from Clostridium Perfringens Bound to Vitamin B12== | | ==Crystal Structure of the EutL Microcompartment Shell Protein from Clostridium Perfringens Bound to Vitamin B12== |
| - | <StructureSection load='4u6i' size='340' side='right' caption='[[4u6i]], [[Resolution|resolution]] 2.10Å' scene=''> | + | <StructureSection load='4u6i' size='340' side='right'caption='[[4u6i]], [[Resolution|resolution]] 2.10Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4u6i]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_perfringens"_veillon_and_zuber_1898 "bacillus perfringens" veillon and zuber 1898]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4U6I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4U6I FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4u6i]] 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=4U6I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4U6I FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=B12:COBALAMIN'>B12</scene>, <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]] 2.1Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">eutL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1502 "Bacillus perfringens" Veillon and Zuber 1898])</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=B12:COBALAMIN'>B12</scene>, <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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4u6i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4u6i OCA], [http://pdbe.org/4u6i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4u6i RCSB], [http://www.ebi.ac.uk/pdbsum/4u6i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4u6i 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=4u6i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4u6i OCA], [https://pdbe.org/4u6i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4u6i RCSB], [https://www.ebi.ac.uk/pdbsum/4u6i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4u6i ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | + | == 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> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacillus perfringens veillon and zuber 1898]] | + | [[Category: Clostridium perfringens]] |
| - | [[Category: Crowley, C S]] | + | [[Category: Large Structures]] |
| - | [[Category: Kopstein, J S]] | + | [[Category: Crowley CS]] |
| - | [[Category: Thompson, M C]] | + | [[Category: Kopstein JS]] |
| - | [[Category: Yeates, T O]] | + | [[Category: Thompson MC]] |
| - | [[Category: Bacterial microcompartment]] | + | [[Category: Yeates TO]] |
| - | [[Category: Bmc shell protein]]
| + | |
| - | [[Category: Cobalamin]]
| + | |
| - | [[Category: Eut]]
| + | |
| - | [[Category: Transport protein]]
| + | |
| - | [[Category: Vitamin b12]]
| + | |
| Structural highlights
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 EutL shell protein is a key component of the ethanolamine-utilization microcompartment, which serves to compartmentalize ethanolamine degradation in diverse bacteria. The apparent function of this shell protein is to facilitate the selective diffusion of large cofactor molecules between the cytoplasm and the lumen of the microcompartment. While EutL is implicated in molecular-transport phenomena, the details of its function, including the identity of its transport substrate, remain unknown. Here, the 2.1 A resolution X-ray crystal structure of a EutL shell protein bound to cobalamin (vitamin B12) is presented and the potential relevance of the observed protein-ligand interaction is briefly discussed. This work represents the first structure of a bacterial microcompartment shell protein bound to a potentially relevant cofactor molecule.
Structure of a bacterial microcompartment shell protein bound to a cobalamin cofactor.,Thompson MC, Crowley CS, Kopstein J, Bobik TA, Yeates TO Acta Crystallogr F Struct Biol Commun. 2014 Dec 1;70(Pt 12):1584-90. doi:, 10.1107/S2053230X1402158X. Epub 2014 Nov 14. PMID:25484204[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, 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
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