4ddf: Difference between revisions

Revision as of 08:13, 21 September 2022

Computationally Designed Self-assembling Octahedral Cage protein, O333, Crystallized in space group P4

Structural highlights

4ddf is a 12 chain structure with sequence from Salmonella enterica. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	CL, SO4
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[PDUT_SALTY] A minor shell protein of the bacterial microcompartment (BMC) dedicated to 1,2-propanediol (1,2-PD) degradation. The isolated BMC shell component protein ratio for J:A:B':B:K:T:U is approximately 15:10:7:6:1:1:2 (PubMed:12923081). Not required for structural integrity of BMCs nor to mitigate propionaldehyde toxicity, may selectively transport specific metabolites (PubMed:21239588). May be involved in electron transport across the BMC shell (Probable). Can be engineered to alter permeability of the BMC shell (PubMed:31674899).^[1] ^[2] ^[3] ^[4] The 1,2-PD-specific bacterial microcompartment (BMC) concentrates low levels of 1,2-PD catabolic enzymes, concentrates volatile reaction intermediates thus enhancing pathway flux and keeps the level of toxic, mutagenic propionaldehyde low.^[5]

Publication Abstract from PubMed

We describe a general computational method for designing proteins that self-assemble to a desired symmetric architecture. Protein building blocks are docked together symmetrically to identify complementary packing arrangements, and low-energy protein-protein interfaces are then designed between the building blocks in order to drive self-assembly. We used trimeric protein building blocks to design a 24-subunit, 13-nm diameter complex with octahedral symmetry and a 12-subunit, 11-nm diameter complex with tetrahedral symmetry. The designed proteins assembled to the desired oligomeric states in solution, and the crystal structures of the complexes revealed that the resulting materials closely match the design models. The method can be used to design a wide variety of self-assembling protein nanomaterials.

Computational design of self-assembling protein nanomaterials with atomic level accuracy.,King NP, Sheffler W, Sawaya MR, Vollmar BS, Sumida JP, Andre I, Gonen T, Yeates TO, Baker D Science. 2012 Jun 1;336(6085):1171-4. PMID:22654060^[6]

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

References

↑ Havemann GD, Bobik TA. Protein content of polyhedral organelles involved in coenzyme B12-dependent degradation of 1,2-propanediol in Salmonella enterica serovar Typhimurium LT2. J Bacteriol. 2003 Sep;185(17):5086-95. PMID:12923081
↑ Cheng S, Sinha S, Fan C, Liu Y, Bobik TA. Genetic analysis of the protein shell of the microcompartments involved in coenzyme B12-dependent 1,2-propanediol degradation by Salmonella. J Bacteriol. 2011 Mar;193(6):1385-92. doi: 10.1128/JB.01473-10. Epub 2011 Jan 14. PMID:21239588 doi:https://dx.doi.org/10.1128/JB.01473-10
↑ Chowdhury C, Bobik TA. Engineering the PduT shell protein to modify the permeability of the 1,2-propanediol microcompartment of Salmonella. Microbiology (Reading). 2019 Dec;165(12):1355-1364. doi: 10.1099/mic.0.000872. PMID:31674899 doi:https://dx.doi.org/10.1099/mic.0.000872
↑ Crowley CS, Cascio D, Sawaya MR, Kopstein JS, Bobik TA, Yeates TO. Structural insights into the mechanisms of transport across the Salmonella enterica Pdu microcompartment shell. J Biol Chem. 2010 Sep 24. PMID:20870711 doi:10.1074/jbc.M110.160580
↑ Jakobson CM, Tullman-Ercek D, Slininger MF, Mangan NM. A systems-level model reveals that 1,2-Propanediol utilization microcompartments enhance pathway flux through intermediate sequestration. PLoS Comput Biol. 2017 May 5;13(5):e1005525. doi: 10.1371/journal.pcbi.1005525., eCollection 2017 May. PMID:28475631 doi:https://dx.doi.org/10.1371/journal.pcbi.1005525
↑ King NP, Sheffler W, Sawaya MR, Vollmar BS, Sumida JP, Andre I, Gonen T, Yeates TO, Baker D. Computational design of self-assembling protein nanomaterials with atomic level accuracy. Science. 2012 Jun 1;336(6085):1171-4. PMID:22654060 doi:10.1126/science.1219364

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Havemann GD, Bobik TA. Protein content of polyhedral organelles involved in coenzyme B12-dependent degradation of 1,2-propanediol in Salmonella enterica serovar Typhimurium LT2. J Bacteriol. 2003 Sep;185(17):5086-95. PMID:12923081

[2] Cheng S, Sinha S, Fan C, Liu Y, Bobik TA. Genetic analysis of the protein shell of the microcompartments involved in coenzyme B12-dependent 1,2-propanediol degradation by Salmonella. J Bacteriol. 2011 Mar;193(6):1385-92. doi: 10.1128/JB.01473-10. Epub 2011 Jan 14. PMID:21239588 doi:https://dx.doi.org/10.1128/JB.01473-10

[3] Chowdhury C, Bobik TA. Engineering the PduT shell protein to modify the permeability of the 1,2-propanediol microcompartment of Salmonella. Microbiology (Reading). 2019 Dec;165(12):1355-1364. doi: 10.1099/mic.0.000872. PMID:31674899 doi:https://dx.doi.org/10.1099/mic.0.000872

[4] Crowley CS, Cascio D, Sawaya MR, Kopstein JS, Bobik TA, Yeates TO. Structural insights into the mechanisms of transport across the Salmonella enterica Pdu microcompartment shell. J Biol Chem. 2010 Sep 24. PMID:20870711 doi:10.1074/jbc.M110.160580

[5] Jakobson CM, Tullman-Ercek D, Slininger MF, Mangan NM. A systems-level model reveals that 1,2-Propanediol utilization microcompartments enhance pathway flux through intermediate sequestration. PLoS Comput Biol. 2017 May 5;13(5):e1005525. doi: 10.1371/journal.pcbi.1005525., eCollection 2017 May. PMID:28475631 doi:https://dx.doi.org/10.1371/journal.pcbi.1005525

[6] King NP, Sheffler W, Sawaya MR, Vollmar BS, Sumida JP, Andre I, Gonen T, Yeates TO, Baker D. Computational design of self-assembling protein nanomaterials with atomic level accuracy. Science. 2012 Jun 1;336(6085):1171-4. PMID:22654060 doi:10.1126/science.1219364

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@@ Line 1: / Line 1: @@
 ==Computationally Designed Self-assembling Octahedral Cage protein, O333, Crystallized in space group P4==
-<StructureSection load='4ddf' size='340' side='right' caption='[[4ddf]], [[Resolution|resolution]] 3.15&Aring;' scene=''>
+<StructureSection load='4ddf' size='340' side='right'caption='[[4ddf]], [[Resolution|resolution]] 3.15&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4ddf]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_cholerae-suis"_smith_1894 "bacillus cholerae-suis" smith 1894]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DDF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4DDF FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4ddf]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Salmonella_enterica Salmonella enterica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DDF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4DDF FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3vcd|3vcd]], [[3n79|3n79]]</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=4ddf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ddf OCA], [https://pdbe.org/4ddf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ddf RCSB], [https://www.ebi.ac.uk/pdbsum/4ddf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ddf ProSAT]</span></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PduT ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=28901 "Bacillus cholerae-suis" Smith 1894])</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ddf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ddf OCA], [http://pdbe.org/4ddf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ddf RCSB], [http://www.ebi.ac.uk/pdbsum/4ddf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ddf ProSAT]</span></td></tr>
 </table>
+== Function ==
+[[https://www.uniprot.org/uniprot/PDUT_SALTY PDUT_SALTY]] A minor shell protein of the bacterial microcompartment (BMC) dedicated to 1,2-propanediol (1,2-PD) degradation. The isolated BMC shell component protein ratio for J:A:B':B:K:T:U is approximately 15:10:7:6:1:1:2 (PubMed:12923081). Not required for structural integrity of BMCs nor to mitigate propionaldehyde toxicity, may selectively transport specific metabolites (PubMed:21239588). May be involved in electron transport across the BMC shell (Probable). Can be engineered to alter permeability of the BMC shell (PubMed:31674899).<ref>PMID:12923081</ref> <ref>PMID:21239588</ref> <ref>PMID:31674899</ref> <ref>PMID:20870711</ref>   The 1,2-PD-specific bacterial microcompartment (BMC) concentrates low levels of 1,2-PD catabolic enzymes, concentrates volatile reaction intermediates thus enhancing pathway flux and keeps the level of toxic, mutagenic propionaldehyde low.<ref>PMID:28475631</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 22: / Line 22: @@
 __TOC__
 </StructureSection>
-[[Category: Bacillus cholerae-suis smith 1894]]
+[[Category: Large Structures]]
-[[Category: Baker, D]]
+[[Category: Salmonella enterica]]
-[[Category: King, N P]]
+[[Category: Baker D]]
-[[Category: Sawaya, M R]]
+[[Category: King NP]]
-[[Category: Sheffler, W]]
+[[Category: Sawaya MR]]
-[[Category: Yeates, T O]]
+[[Category: Sheffler W]]
-[[Category: Electron transport]]
+[[Category: Yeates TO]]
-[[Category: Self assembling octahedral cage design]]

4ddf: Difference between revisions

Revision as of 08:13, 21 September 2022

Computationally Designed Self-assembling Octahedral Cage protein, O333, Crystallized in space group P4

Structural highlights

Function

Publication Abstract from PubMed

References

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