6wkv: Difference between revisions

Latest revision as of 14:44, 6 March 2024

Cryo-EM structure of engineered variant of the Encapsulin from Thermotoga maritima (TmE)

Structural highlights

6wkv is a 60 chain structure with sequence from Thermotoga maritima. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Electron Microscopy, Resolution 2.99Å
Ligands:	FMN
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

ENCAP_THEMA Shell component of a type 1 encapsulin nanocompartment. Assembles into proteinaceous shells 23-24 nm in diameter with 2-2.5 nm thick walls. Cargo protein Flp (ferritin-like protein, may store iron) is targeted to the interior via its C-terminal extension; empty intact shells can be isolated in the absence of cargo protein (PubMed:19172747, PubMed:27224728, PubMed:32961724, PubMed:30376298, PubMed:33769792, PubMed:33953921, PubMed:34815415). Fe(2+) may be able to pass though the 5-fold and dimer channels in the protein shell (Probable).^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7] ^[8] Protease that exhibits activity toward chymotrypsin and trypsin substrates (PubMed:9872409, PubMed:11210524). Probably does not have antibacterial activity (Probable).^[9] ^[10] ^[11]

References

↑ Sutter M, Boehringer D, Gutmann S, Gunther S, Prangishvili D, Loessner MJ, Stetter KO, Weber-Ban E, Ban N. Structural basis of enzyme encapsulation into a bacterial nanocompartment. Nat Struct Mol Biol. 2008 Sep;15(9):939-47. PMID:19172747
↑ Cassidy-Amstutz C, Oltrogge L, Going CC, Lee A, Teng P, Quintanilla D, East-Seletsky A, Williams ER, Savage DF. Identification of a Minimal Peptide Tag for in Vivo and in Vitro Loading of Encapsulin. Biochemistry. 2016 Jun 21;55(24):3461-8. PMID:27224728 doi:10.1021/acs.biochem.6b00294
↑ Williams EM, Jung SM, Coffman JL, Lutz S. Pore Engineering for Enhanced Mass Transport in Encapsulin Nanocompartments. ACS Synth Biol. 2018 Nov 16;7(11):2514-2517. PMID:30376298 doi:10.1021/acssynbio.8b00295
↑ Xiong X, Sun C, Vago FS, Klose T, Zhu J, Jiang W. Cryo-EM Structure of Heterologous Protein Complex Loaded Thermotoga Maritima Encapsulin Capsid. Biomolecules. 2020 Sep 19;10(9):1342. PMID:32961724 doi:10.3390/biom10091342
↑ Jenkins MC, Lutz S. Encapsulin Nanocontainers as Versatile Scaffolds for the Development of Artificial Metabolons. ACS Synth Biol. 2021 Apr 16;10(4):857-869. PMID:33769792 doi:10.1021/acssynbio.0c00636
↑ Wiryaman T, Toor N. Cryo-EM structure of a thermostable bacterial nanocompartment. IUCrJ. 2021 Apr 2;8(Pt 3):342-350. doi: 10.1107/S2052252521001949. eCollection, 2021 May 1. PMID:33953921 doi:https://dx.doi.org/10.1107/S2052252521001949
↑ LaFrance BJ, Cassidy-Amstutz C, Nichols RJ, Oltrogge LM, Nogales E, Savage DF. The encapsulin from Thermotoga maritima is a flavoprotein with a symmetry matched ferritin-like cargo protein. Sci Rep. 2021 Nov 23;11(1):22810. doi: 10.1038/s41598-021-01932-w. PMID:34815415 doi:https://dx.doi.org/10.1038/s41598-021-01932-w
↑ Wiryaman T, Toor N. Cryo-EM structure of a thermostable bacterial nanocompartment. IUCrJ. 2021 Apr 2;8(Pt 3):342-350. doi: 10.1107/S2052252521001949. eCollection, 2021 May 1. PMID:33953921 doi:https://dx.doi.org/10.1107/S2052252521001949
↑ Hicks PM, Chang LS, Kelly RM. Homomultimeric protease and putative bacteriocin homolog from Thermotoga maritima. Methods Enzymol. 2001;330:455-60. PMID:11210524 doi:10.1016/s0076-6879(01)30397-x
↑ Hicks PM, Rinker KD, Baker JR, Kelly RM. Homomultimeric protease in the hyperthermophilic bacterium Thermotoga maritima has structural and amino acid sequence homology to bacteriocins in mesophilic bacteria. FEBS Lett. 1998 Dec 4;440(3):393-8. PMID:9872409 doi:10.1016/s0014-5793(98)01451-3
↑ Sutter M, Boehringer D, Gutmann S, Gunther S, Prangishvili D, Loessner MJ, Stetter KO, Weber-Ban E, Ban N. Structural basis of enzyme encapsulation into a bacterial nanocompartment. Nat Struct Mol Biol. 2008 Sep;15(9):939-47. PMID:19172747

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Sutter M, Boehringer D, Gutmann S, Gunther S, Prangishvili D, Loessner MJ, Stetter KO, Weber-Ban E, Ban N. Structural basis of enzyme encapsulation into a bacterial nanocompartment. Nat Struct Mol Biol. 2008 Sep;15(9):939-47. PMID:19172747

[2] Cassidy-Amstutz C, Oltrogge L, Going CC, Lee A, Teng P, Quintanilla D, East-Seletsky A, Williams ER, Savage DF. Identification of a Minimal Peptide Tag for in Vivo and in Vitro Loading of Encapsulin. Biochemistry. 2016 Jun 21;55(24):3461-8. PMID:27224728 doi:10.1021/acs.biochem.6b00294

[3] Williams EM, Jung SM, Coffman JL, Lutz S. Pore Engineering for Enhanced Mass Transport in Encapsulin Nanocompartments. ACS Synth Biol. 2018 Nov 16;7(11):2514-2517. PMID:30376298 doi:10.1021/acssynbio.8b00295

[4] Xiong X, Sun C, Vago FS, Klose T, Zhu J, Jiang W. Cryo-EM Structure of Heterologous Protein Complex Loaded Thermotoga Maritima Encapsulin Capsid. Biomolecules. 2020 Sep 19;10(9):1342. PMID:32961724 doi:10.3390/biom10091342

[5] Jenkins MC, Lutz S. Encapsulin Nanocontainers as Versatile Scaffolds for the Development of Artificial Metabolons. ACS Synth Biol. 2021 Apr 16;10(4):857-869. PMID:33769792 doi:10.1021/acssynbio.0c00636

[6] Wiryaman T, Toor N. Cryo-EM structure of a thermostable bacterial nanocompartment. IUCrJ. 2021 Apr 2;8(Pt 3):342-350. doi: 10.1107/S2052252521001949. eCollection, 2021 May 1. PMID:33953921 doi:https://dx.doi.org/10.1107/S2052252521001949

[7] LaFrance BJ, Cassidy-Amstutz C, Nichols RJ, Oltrogge LM, Nogales E, Savage DF. The encapsulin from Thermotoga maritima is a flavoprotein with a symmetry matched ferritin-like cargo protein. Sci Rep. 2021 Nov 23;11(1):22810. doi: 10.1038/s41598-021-01932-w. PMID:34815415 doi:https://dx.doi.org/10.1038/s41598-021-01932-w

[8] Wiryaman T, Toor N. Cryo-EM structure of a thermostable bacterial nanocompartment. IUCrJ. 2021 Apr 2;8(Pt 3):342-350. doi: 10.1107/S2052252521001949. eCollection, 2021 May 1. PMID:33953921 doi:https://dx.doi.org/10.1107/S2052252521001949

[9] Hicks PM, Chang LS, Kelly RM. Homomultimeric protease and putative bacteriocin homolog from Thermotoga maritima. Methods Enzymol. 2001;330:455-60. PMID:11210524 doi:10.1016/s0076-6879(01)30397-x

[10] Hicks PM, Rinker KD, Baker JR, Kelly RM. Homomultimeric protease in the hyperthermophilic bacterium Thermotoga maritima has structural and amino acid sequence homology to bacteriocins in mesophilic bacteria. FEBS Lett. 1998 Dec 4;440(3):393-8. PMID:9872409 doi:10.1016/s0014-5793(98)01451-3

[11] Sutter M, Boehringer D, Gutmann S, Gunther S, Prangishvili D, Loessner MJ, Stetter KO, Weber-Ban E, Ban N. Structural basis of enzyme encapsulation into a bacterial nanocompartment. Nat Struct Mol Biol. 2008 Sep;15(9):939-47. PMID:19172747

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 6wkv is ON HOLD
+==Cryo-EM structure of engineered variant of the Encapsulin from Thermotoga maritima (TmE)==
+<StructureSection load='6wkv' size='340' side='right'caption='[[6wkv]], [[Resolution|resolution]] 2.99&Aring;' scene=''>
-Authors: Williams, E., Jenkins, M., Zhao, H., Juneja, P., Lutz, S.
+== Structural highlights ==
+<table><tr><td colspan='2'>[[6wkv]] is a 60 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6WKV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6WKV FirstGlance]. <br>
-Description: Cryo-EM structure of engineered variant of the Encapsulin from Thermotoga maritima (TmE)
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 2.99&#8491;</td></tr>
-[[Category: Unreleased Structures]]
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene></td></tr>
-[[Category: Jenkins, M]]
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6wkv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6wkv OCA], [https://pdbe.org/6wkv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6wkv RCSB], [https://www.ebi.ac.uk/pdbsum/6wkv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6wkv ProSAT]</span></td></tr>
-[[Category: Juneja, P]]
+</table>
-[[Category: Zhao, H]]
+== Function ==
-[[Category: Williams, E]]
+[https://www.uniprot.org/uniprot/ENCAP_THEMA ENCAP_THEMA] Shell component of a type 1 encapsulin nanocompartment. Assembles into proteinaceous shells 23-24 nm in diameter with 2-2.5 nm thick walls. Cargo protein Flp (ferritin-like protein, may store iron) is targeted to the interior via its C-terminal extension; empty intact shells can be isolated in the absence of cargo protein (PubMed:19172747, PubMed:27224728, PubMed:32961724, PubMed:30376298, PubMed:33769792, PubMed:33953921, PubMed:34815415). Fe(2+) may be able to pass though the 5-fold and dimer channels in the protein shell (Probable).<ref>PMID:19172747</ref> <ref>PMID:27224728</ref> <ref>PMID:30376298</ref> <ref>PMID:32961724</ref> <ref>PMID:33769792</ref> <ref>PMID:33953921</ref> <ref>PMID:34815415</ref> <ref>PMID:33953921</ref>   Protease that exhibits activity toward chymotrypsin and trypsin substrates (PubMed:9872409, PubMed:11210524). Probably does not have antibacterial activity (Probable).<ref>PMID:11210524</ref> <ref>PMID:9872409</ref> <ref>PMID:19172747</ref>
-[[Category: Lutz, S]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
+[[Category: Thermotoga maritima]]
+[[Category: Jenkins M]]
+[[Category: Juneja P]]
+[[Category: Lutz S]]
+[[Category: Williams E]]
+[[Category: Zhao H]]

6wkv: Difference between revisions

Latest revision as of 14:44, 6 March 2024

Cryo-EM structure of engineered variant of the Encapsulin from Thermotoga maritima (TmE)

Structural highlights

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