View source for 7zgy


==S-layer Deinoxanthin Binding Complex, C3 symmetry==
<StructureSection load='7zgy' size='340' side='right'caption='[[7zgy]], [[Resolution|resolution]] 2.54&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[7zgy]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Deinococcus_radiodurans_R1 Deinococcus radiodurans R1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7ZGY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ZGY FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 2.54&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=JPI:(3~{S},5~{R},6~{R})-5-[(3~{S},7~{R},12~{S},16~{S},20~{S})-3,7,12,16,20,24-hexamethyl-24-oxidanyl-pentacosyl]-4,4,6-trimethyl-cyclohexane-1,3-diol'>JPI</scene>, <scene name='pdbligand=JPX:[(2~{S})-3-[[(2~{S})-3-[(2~{S},3~{S},4~{S},5~{S},6~{S})-6-(hydroxymethyl)-4,5-bis(oxidanyl)-3-(propanoylamino)oxan-2-yl]oxy-1-oxidanylidene-1-(pentadecylamino)propan-2-yl]oxy-oxidanyl-phosphoryl]oxy-2-octanoyloxy-propyl]+decanoate'>JPX</scene>, <scene name='pdbligand=JQ6:[(2~{S})-2-acetyloxy-3-[[(2~{S})-3-[(2~{R},3~{S},4~{S},5~{S},6~{S})-6-(hydroxymethyl)-3-(octadecanoylamino)-4,5-bis(oxidanyl)oxan-2-yl]oxy-1-oxidanylidene-1-(pentylamino)propan-2-yl]oxy-oxidanyl-phosphoryl]oxy-propyl]+ethanoate'>JQ6</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=7zgy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7zgy OCA], [https://pdbe.org/7zgy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7zgy RCSB], [https://www.ebi.ac.uk/pdbsum/7zgy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7zgy ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/SLPA_DEIRA SLPA_DEIRA] Plays an important role in the structural organization and integrity of the cell envelope, bridging the outer membrane to the peptidoglyan layer (PubMed:16946272, PubMed:26074883, PubMed:35943982). Is a highly abundant molecule in the D.radiodurans cell envelope but is not a fundamental component of the S-layer (PubMed:35943982). Binds the carotenoid deinoxanthin, a strong protective antioxidant specific of this bacterium, and could be part of the first lane of defense against UV radiation, especially under desiccation (PubMed:26909071). Appears to be a nonselective channel (PubMed:32071085). Is able to transport charged amino acids such as Lys, Arg and Glu; the large dimension of the pore points toward the physiological importance of the SDBC complex in assisting and allowing the exchange of substances, including nutrients, with the surrounding environment (PubMed:35577074).<ref>PMID:16946272</ref> <ref>PMID:26074883</ref> <ref>PMID:26909071</ref> <ref>PMID:32071085</ref> <ref>PMID:35577074</ref> <ref>PMID:35943982</ref> 
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The radiation-resistant bacterium Deinococcus radiodurans is known as the world's toughest bacterium. The S-layer of D. radiodurans, consisting of several proteins on the surface of the cellular envelope and intimately associated with the outer membrane, has therefore been useful as a model for structural and functional studies. Its main proteinaceous unit, the S-layer deinoxanthin-binding complex (SDBC), is a hetero-oligomeric assembly known to contribute to the resistance against environmental stress and have porin functional features; however, its precise structure is unknown. Here, we resolved the structure of the SDBC at approximately 2.5 A resolution by cryo-EM and assigned the sequence of its main subunit, the protein DR_2577. This structure is characterized by a pore region, a massive beta-barrel organization, a stalk region consisting of a trimeric coiled coil, and a collar region at the base of the stalk. We show that each monomer binds three Cu ions and one Fe ion and retains one deinoxanthin molecule and two phosphoglycolipids, all exclusive to D. radiodurans. Finally, electrophysiological characterization of the SDBC shows that it exhibits transport properties with several amino acids. Taken together, these results highlight the SDBC as a robust structure displaying both protection and sieving functions that facilitates exchanges with the environment.

The cryo-EM structure of the S-layer deinoxanthin-binding complex of Deinococcus radiodurans informs properties of its environmental interactions.,Farci D, Haniewicz P, de Sanctis D, Iesu L, Kereiche S, Winterhalter M, Piano D J Biol Chem. 2022 Jun;298(6):102031. doi: 10.1016/j.jbc.2022.102031. Epub 2022 , May 13. PMID:35577074<ref>PMID:35577074</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 7zgy" style="background-color:#fffaf0;"></div>
== References ==
<references/>
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</StructureSection>
[[Category: Deinococcus radiodurans R1]]
[[Category: Large Structures]]
[[Category: Farci D]]
[[Category: Piano D]]