8agd

From Proteopedia

(Difference between revisions)

Current revision

Full SDBC and SOD assembly

Structural highlights

8agd is a 6 chain structure with sequence from Deinococcus radiodurans R1. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Electron Microscopy, Resolution 3.5Å
Ligands:	, , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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).^[1] ^[2] ^[3] ^[4] ^[5] ^[6]

Publication Abstract from PubMed

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 approximately 280 A, 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.

The SDBC is active in quenching oxidative conditions and bridges the cell envelope layers in Deinococcus radiodurans.,Farci D, Graca AT, Iesu L, de Sanctis D, Piano D J Biol Chem. 2023 Jan;299(1):102784. doi: 10.1016/j.jbc.2022.102784. Epub 2022 , Dec 9. PMID:36502921^[7]

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

References

↑ Rothfuss H, Lara JC, Schmid AK, Lidstrom ME. Involvement of the S-layer proteins Hpi and SlpA in the maintenance of cell envelope integrity in Deinococcus radiodurans R1. Microbiology (Reading). 2006 Sep;152(Pt 9):2779-2787. doi: 10.1099/mic.0.28971-0. PMID:16946272 doi:http://dx.doi.org/10.1099/mic.0.28971-0
↑ Farci D, Bowler MW, Esposito F, McSweeney S, Tramontano E, Piano D. Purification and characterization of DR_2577 (SlpA) a major S-layer protein from Deinococcus radiodurans. Front Microbiol. 2015 Jun 3;6:414. doi: 10.3389/fmicb.2015.00414. eCollection, 2015. PMID:26074883 doi:http://dx.doi.org/10.3389/fmicb.2015.00414
↑ Farci D, Slavov C, Tramontano E, Piano D. The S-layer Protein DR_2577 Binds Deinoxanthin and under Desiccation Conditions Protects against UV-Radiation in Deinococcus radiodurans. Front Microbiol. 2016 Feb 16;7:155. doi: 10.3389/fmicb.2016.00155. eCollection, 2016. PMID:26909071 doi:http://dx.doi.org/10.3389/fmicb.2016.00155
↑ Farci D, Aksoyoglu MA, Farci SF, Bafna JA, Bodrenko I, Ceccarelli M, Kirkpatrick J, Winterhalter M, Kereïche S, Piano D. Structural insights into the main S-layer unit of Deinococcus radiodurans reveal a massive protein complex with porin-like features. J Biol Chem. 2020 Mar 27;295(13):4224-4236. PMID:32071085 doi:10.1074/jbc.RA119.012174
↑ Farci D, Haniewicz P, de Sanctis D, Iesu L, Kereïche S, Winterhalter M, Piano D. The cryo-EM structure of the S-layer deinoxanthin-binding complex of Deinococcus radiodurans informs properties of its environmental interactions. J Biol Chem. 2022 Jun;298(6):102031. PMID:35577074 doi:10.1016/j.jbc.2022.102031
↑ von Kugelgen A, van Dorst S, Alva V, Bharat TAM. A multidomain connector links the outer membrane and cell wall in phylogenetically deep-branching bacteria. Proc Natl Acad Sci U S A. 2022 Aug 16;119(33):e2203156119. doi: , 10.1073/pnas.2203156119. Epub 2022 Aug 9. PMID:35943982 doi:http://dx.doi.org/10.1073/pnas.2203156119
↑ Farci D, Graça AT, Iesu L, de Sanctis D, Piano D. The SDBC is active in quenching oxidative conditions and bridges the cell envelope layers in Deinococcus radiodurans. J Biol Chem. 2023 Jan;299(1):102784. PMID:36502921 doi:10.1016/j.jbc.2022.102784

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/8agd"

Categories: Deinococcus radiodurans R1 | Large Structures | Farci D | Graca AT | Piano D

@@ Line 4: / Line 4: @@
 == Structural highlights ==
 <table><tr><td colspan='2'>[[8agd]] is a 6 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=8AGD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8AGD FirstGlance]. <br>
-</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>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3.5&#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=8agd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8agd OCA], [https://pdbe.org/8agd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8agd RCSB], [https://www.ebi.ac.uk/pdbsum/8agd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8agd ProSAT]</span></td></tr>
 </table>
 == Function ==
-[https://www.uniprot.org/uniprot/SLPA_DEIRA SLPA_DEIRA] Major constituent of the S-layer. Plays an important role in the structural organization and integrity of the S-layer (PubMed:16946272, PubMed:26074883). 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).<ref>PMID:16946272</ref> <ref>PMID:26074883</ref> <ref>PMID:26909071</ref>
+[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 ==

8agd

From Proteopedia

Current revision

Full SDBC and SOD assembly

Structural highlights

Function

Publication Abstract from PubMed

References

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