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TitleThe cryo-EM structure of the S-layer deinoxanthin-binding complex of Deinococcus radiodurans informs properties of its environmental interactions.
Journal, issue, pagesJ Biol Chem, Vol. 298, Issue 6, Page 102031, Year 2022
Publish dateMay 13, 2022
AuthorsDomenica Farci / Patrycja Haniewicz / Daniele de Sanctis / Luca Iesu / Sami Kereïche / Mathias Winterhalter / Dario Piano /
PubMed AbstractThe 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 ...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 ∼2.5 Å 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 β-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.
External linksJ Biol Chem / PubMed:35577074 / PubMed Central
MethodsEM (single particle)
Resolution2.54 - 2.88 Å
Structure data

14714

7zgx

EMDB-14714, PDB-7zgx:
S-layer Deinoxanthin Binding Complex, C1 symmetry
Method: EM (single particle) / Resolution: 2.88 Å

14715

7zgy

EMDB-14715, PDB-7zgy:
S-layer Deinoxanthin Binding Complex, C3 symmetry
Method: EM (single particle) / Resolution: 2.54 Å

Chemicals

ChemComp-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

ChemComp-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

ChemComp-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

ChemComp-CU:
COPPER (II) ION / Copper

ChemComp-FE:
Unknown entry / Iron

Source
  • deinococcus radiodurans r1 (radioresistant)
KeywordsSTRUCTURAL PROTEIN / PROTEIN / S-layer / deinococcus radiodurans / DR_2577 / S-layer Deinoxanthin Binding Complex

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