3n79: Difference between revisions

Latest revision as of 10:28, 21 February 2024

PduT C38S Mutant from Salmonella enterica Typhimurium

Structural highlights

3n79 is a 1 chain structure with sequence from Salmonella enterica subsp. enterica serovar Typhimurium. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.5Å
Ligands:	CL, NA, 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]

Evolutionary Conservation

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

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

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

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[2]

[3]

[4]

[5]

@@ Line 1: / Line 1: @@
-{{STRUCTURE_3n79|  PDB=3n79  |  SCENE=  }}
-===PduT C38S Mutant from Salmonella enterica Typhimurium===
-{{ABSTRACT_PUBMED_20870711}}
-==About this Structure==
+==PduT C38S Mutant from Salmonella enterica Typhimurium==
-[[3n79]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_typhimurium Salmonella enterica subsp. enterica serovar typhimurium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3N79 OCA].
+<StructureSection load='3n79' size='340' side='right'caption='[[3n79]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
+== Structural highlights ==
-==Reference==
+<table><tr><td colspan='2'>[[3n79]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_Typhimurium Salmonella enterica subsp. enterica serovar Typhimurium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3N79 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3N79 FirstGlance]. <br>
-<ref group="xtra">PMID:020870711</ref><references group="xtra"/><references/>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.5&#8491;</td></tr>
-[[Category: Salmonella enterica subsp. enterica serovar typhimurium]]
+<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=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-[[Category: Cascio, D.]]
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3n79 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3n79 OCA], [https://pdbe.org/3n79 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3n79 RCSB], [https://www.ebi.ac.uk/pdbsum/3n79 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3n79 ProSAT]</span></td></tr>
-[[Category: Crowley, C S.]]
+</table>
-[[Category: Sawaya, M R.]]
+== Function ==
-[[Category: Yeates, T O.]]
+[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>
-[[Category: Bmc shell protein]]
+== Evolutionary Conservation ==
-[[Category: Carboxysome]]
+[[Image:Consurf_key_small.gif|200px|right]]
-[[Category: Electron transport]]
+Check<jmol>
-[[Category: Fes cluster]]
+  <jmolCheckbox>
-[[Category: Pdu]]
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/n7/3n79_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</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=3n79 ConSurf].
+<div style="clear:both"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
+[[Category: Salmonella enterica subsp. enterica serovar Typhimurium]]
+[[Category: Cascio D]]
+[[Category: Crowley CS]]
+[[Category: Sawaya MR]]
+[[Category: Yeates TO]]

3n79: Difference between revisions

Latest revision as of 10:28, 21 February 2024

PduT C38S Mutant from Salmonella enterica Typhimurium

Structural highlights

Function

Evolutionary Conservation

References

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