EMDB/PDB/SASBDBから引用されている文献のデータベース

キーワード
構造解析手法	All X線回折 NMR 電子顕微鏡小角散乱中性子線回折線維回折粉末回折赤外分光 EPR FRET 理論モデルハイブリッド
著者・登録者
ジャーナル
IF	>30 >20 >10 >5 all

タイトル	The SDBC is active in quenching oxidative conditions and bridges the cell envelope layers in Deinococcus radiodurans.
ジャーナル・号・ページ	J Biol Chem, Vol. 299, Issue 1, Page 102784, Year 2023
掲載日	2022年12月9日
著者	Domenica Farci / André T Graça / Luca Iesu / Daniele de Sanctis / Dario Piano /
PubMed 要旨	Deinococcus radiodurans is known for its remarkable ability to withstand harsh stressful conditions. The outermost layer of its cell envelope is a proteinaceous coat, the S-layer, essential for ...Deinococcus radiodurans is known for its remarkable ability to withstand harsh stressful conditions. The outermost layer of its cell envelope is a proteinaceous coat, the S-layer, essential for resistance to and interactions with the environment. The S-layer Deinoxanthin-binding complex (SDBC), one of the main units of the characteristic multilayered cell envelope of this bacterium, protects against environmental stressors and allows exchanges with the environment. So far, specific regions of this complex, the collar and the stalk, remained unassigned. Here, these regions are resolved by cryo-EM and locally refined. The resulting 3D map shows that the collar region of this multiprotein complex is a trimer of the protein DR_0644, a Cu-only superoxide dismutase (SOD) identified here to be efficient in quenching reactive oxygen species. The same data also showed that the stalk region consists of a coiled coil that extends into the cell envelope for ∼280 Å, reaching the inner membrane. Finally, the orientation and localization of the complex are defined by in situ cryo-electron crystallography. The structural organization of the SDBC couples fundamental UV antenna properties with the presence of a Cu-only SOD, showing here coexisting photoprotective and chemoprotective functions. These features suggests how the SDBC and similar protein complexes, might have played a primary role as evolutive templates for the origin of photoautotrophic processes by combining primary protective needs with more independent energetic strategies.
リンク	J Biol Chem / PubMed:36502921 / PubMed Central
手法	EM (単粒子)
解像度	2.54 - 5.3 Å
構造データ	15382 8agd EMDB-15382: S-layer Deinoxanthin-Binding Complex, details of the stalk region PDB-8agd: Full SDBC and SOD assembly 手法: EM (単粒子) / 解像度: 3.5 Å EMDB-15384: S-layer Deinoxanthin-Binding Complex, details of the N-terminal end of the stalk region 手法: EM (単粒子) / 解像度: 5.3 Å EMDB-15487: SDBC and SOD assembly, composite map 手法: EM (単粒子) / 解像度: 3.5 Å PDB-8aca: SDBC DR_0644 subunit, only-Cu Superoxide Dismutase 手法: ELECTRON MICROSCOPY / 解像度: 2.54 Å PDB-8acq: S-layer Deinoxanthin-Binding Complex (SDBC), subunit DR_2577 assembled with its SOD DR_0644 手法: ELECTRON MICROSCOPY / 解像度: 2.54 Å
化合物	ChemComp-CU: COPPER (II) ION / 銅 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-FE: Unknown entry / 鉄
由来	deinococcus radiodurans r1 (放射線耐性)
キーワード	METAL BINDING PROTEIN / Superoxide Dismutase (スーパーオキシドディスムターゼ) / S-layer Deinoxanthin-Binding Complex / Deinococcus radiodurans (デイノコッカス・ラディオデュランス) / Cell envelop / S-layer (S層) / STRUCTURAL PROTEIN (タンパク質) / metal binding proteins / deinoxanthin / phosphoglycolipids / copper (銅) / iron (鉄)