3dkt: Difference between revisions

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== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3dkt]] is a 20 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. The June 2009 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Vaults''  by David Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2009_6 10.2210/rcsb_pdb/mom_2009_6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DKT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DKT FirstGlance]. <br>
<table><tr><td colspan='2'>[[3dkt]] is a 20 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. The June 2009 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Vaults''  by David Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2009_6 10.2210/rcsb_pdb/mom_2009_6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DKT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DKT FirstGlance]. <br>
</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=3dkt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dkt OCA], [https://pdbe.org/3dkt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dkt RCSB], [https://www.ebi.ac.uk/pdbsum/3dkt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dkt ProSAT]</span></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.104&#8491;</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=3dkt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dkt OCA], [https://pdbe.org/3dkt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dkt RCSB], [https://www.ebi.ac.uk/pdbsum/3dkt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dkt ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/MARIT_THEMA MARIT_THEMA]] Protease that exhibits activity toward chymotrypsin and trypsin substrates. May have antibacterial activity.  
[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>
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3dkt ConSurf].
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3dkt ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Compartmentalization is an important organizational feature of life. It occurs at varying levels of complexity ranging from eukaryotic organelles and the bacterial microcompartments, to the molecular reaction chambers formed by enzyme assemblies. The structural basis of enzyme encapsulation in molecular compartments is poorly understood. Here we show, using X-ray crystallographic, biochemical and EM experiments, that a widespread family of conserved bacterial proteins, the linocin-like proteins, form large assemblies that function as a minimal compartment to package enzymes. We refer to this shell-forming protein as 'encapsulin'. The crystal structure of such a particle from Thermotoga maritima determined at 3.1-angstroms resolution reveals that 60 copies of the monomer assemble into a thin, icosahedral shell with a diameter of 240 angstroms. The interior of this nanocompartment is lined with conserved binding sites for short polypeptide tags present as C-terminal extensions of enzymes involved in oxidative-stress response.
Structural basis of enzyme encapsulation into a bacterial nanocompartment.,Sutter M, Boehringer D, Gutmann S, Gunther S, Prangishvili D, Loessner MJ, Stetter KO, Weber-Ban E, Ban N Nat Struct Mol Biol. 2008 Sep;15(9):939-47. PMID:19172747<ref>PMID:19172747</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3dkt" style="background-color:#fffaf0;"></div>
== References ==
== References ==
<references/>
<references/>
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[[Category: Thermotoga maritima]]
[[Category: Thermotoga maritima]]
[[Category: Vaults]]
[[Category: Vaults]]
[[Category: Ban, N]]
[[Category: Ban N]]
[[Category: Boehringer, D]]
[[Category: Boehringer D]]
[[Category: Gutmann, S]]
[[Category: Gutmann S]]
[[Category: Sutter, M]]
[[Category: Sutter M]]
[[Category: Weber-Ban, E]]
[[Category: Weber-Ban E]]
[[Category: Antibiotic]]
[[Category: Antimicrobial]]
[[Category: Bacteriocin]]
[[Category: Cobalt]]
[[Category: Enzyme encapsulation]]
[[Category: Ferritin-like protein]]
[[Category: Hk97-fold]]
[[Category: Hydrolase]]
[[Category: Nanocompartment]]
[[Category: Oxidative stress]]
[[Category: Protease]]
[[Category: Secreted]]
[[Category: Structural protein-virus like particle complex]]

Latest revision as of 11:24, 20 March 2024

Crystal structure of Thermotoga maritima encapsulinCrystal structure of Thermotoga maritima encapsulin

Structural highlights

3dkt is a 20 chain structure with sequence from Thermotoga maritima. The June 2009 RCSB PDB Molecule of the Month feature on Vaults by David Goodsell is 10.2210/rcsb_pdb/mom_2009_6. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 3.104Å
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]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

References

  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:http://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:http://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:http://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

3dkt, resolution 3.10Å

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