5d6v

From Proteopedia

(Difference between revisions)

Current revision

PduJ K25A mutant, from Salmonella enterica serovar Typhimurium LT2, PduJ mutant

Structural highlights

5d6v is a 1 chain structure with sequence from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.5Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PDUJ_SALTY One of the major shell proteins 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). At least one of PduA or PduJ is required for BMC assembly; it must be encoded as the first gene in the pdu operon (PubMed:33227310, PubMed:27561553). Required for structural integrity of BMCs and to mitigate propionaldehyde toxicity, probably joins facets responsible for BMC closure (PubMed:21239588). Edge residues (particularly Lys-25) are important for function and assembly of the BMC (PubMed:24747050). 80% identical to PduA; although their pore regions appear structurally identical, unlike PduA plays no role in 1,2-PD diffusion into or out of the BMC shell. If pduJ is cloned in the chromosomal position of pduA it is able to complement a pduA deletion; it then has a functional pore as it assumes the transport functions of PduA (PubMed:27561553). Overexpression of this protein leads to aberrant filaments that extend the length of the cell, cross the cleavage furrow and impair division. The filaments form nanotubes with a hollow center (PubMed:33227310). Modeling suggests PduJ is probably the hub for binding multiple enzymes to the interior of the BMC; modeling suggests PduC, PduD, PduG and PduM are targeted to PduJ (Probable).^[1] ^[2] ^[3] ^[4] ^[5] ^[6] The 1,2-propanediol (1,2-PD) degradation 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.^[7] ^[8]

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:http://dx.doi.org/10.1128/JB.01473-10
↑ Sinha S, Cheng S, Sung YW, McNamara DE, Sawaya MR, Yeates TO, Bobik TA. Alanine Scanning Mutagenesis Identifies an Asparagine-Arginine-Lysine Triad Essential to Assembly of the Shell of the Pdu Microcompartment. J Mol Biol. 2014 Apr 18. pii: S0022-2836(14)00196-X. doi:, 10.1016/j.jmb.2014.04.012. PMID:24747050 doi:http://dx.doi.org/10.1016/j.jmb.2014.04.012
↑ Chowdhury C, Chun S, Sawaya MR, Yeates TO, Bobik TA. The function of the PduJ microcompartment shell protein is determined by the genomic position of its encoding gene. Mol Microbiol. 2016 Sep;101(5):770-83. doi: 10.1111/mmi.13423. Epub 2016 Jun 7. PMID:27561553 doi:http://dx.doi.org/10.1111/mmi.13423
↑ Kennedy NW, Ikonomova SP, Slininger Lee M, Raeder HW, Tullman-Ercek D. Self-assembling Shell Proteins PduA and PduJ have Essential and Redundant Roles in Bacterial Microcompartment Assembly. J Mol Biol. 2021 Jan 22;433(2):166721. PMID:33227310 doi:10.1016/j.jmb.2020.11.020
↑ Jorda J, Liu Y, Bobik TA, Yeates TO. Exploring bacterial organelle interactomes: a model of the protein-protein interaction network in the Pdu microcompartment. PLoS Comput Biol. 2015 Feb 3;11(2):e1004067. PMID:25646976 doi:10.1371/journal.pcbi.1004067
↑ Sampson EM, Bobik TA. Microcompartments for B12-dependent 1,2-propanediol degradation provide protection from DNA and cellular damage by a reactive metabolic intermediate. J Bacteriol. 2008 Apr;190(8):2966-71. PMID:18296526 doi:10.1128/JB.01925-07
↑ 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:http://dx.doi.org/10.1371/journal.pcbi.1005525

1 Structural highlights
2 Function
3 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5d6v"

Categories: Large Structures | Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 | Chun S | Sawaya MR | Yeates TO

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 5d6v is ON HOLD
+==PduJ K25A mutant, from Salmonella enterica serovar Typhimurium LT2, PduJ mutant==
+<StructureSection load='5d6v' size='340' side='right'caption='[[5d6v]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
-Authors: Chun, S., Sawaya, M.R., Yeates, T.O.
+== Structural highlights ==
+<table><tr><td colspan='2'>[[5d6v]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_Typhimurium_str._LT2 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D6V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5D6V FirstGlance]. <br>
-Description: PduJ K25A mutant, from Salmonella enterica serovar Typhimurium LT2, PduJ mutant
+</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: Unreleased Structures]]
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5d6v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d6v OCA], [https://pdbe.org/5d6v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5d6v RCSB], [https://www.ebi.ac.uk/pdbsum/5d6v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5d6v ProSAT]</span></td></tr>
-[[Category: Sawaya, M.R]]
+</table>
-[[Category: Yeates, T.O]]
+== Function ==
-[[Category: Chun, S]]
+[https://www.uniprot.org/uniprot/PDUJ_SALTY PDUJ_SALTY] One of the major shell proteins 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). At least one of PduA or PduJ is required for BMC assembly; it must be encoded as the first gene in the pdu operon (PubMed:33227310, PubMed:27561553). Required for structural integrity of BMCs and to mitigate propionaldehyde toxicity, probably joins facets responsible for BMC closure (PubMed:21239588). Edge residues (particularly Lys-25) are important for function and assembly of the BMC (PubMed:24747050). 80% identical to PduA; although their pore regions appear structurally identical, unlike PduA plays no role in 1,2-PD diffusion into or out of the BMC shell. If pduJ is cloned in the chromosomal position of pduA it is able to complement a pduA deletion; it then has a functional pore as it assumes the transport functions of PduA (PubMed:27561553). Overexpression of this protein leads to aberrant filaments that extend the length of the cell, cross the cleavage furrow and impair division. The filaments form nanotubes with a hollow center (PubMed:33227310). Modeling suggests PduJ is probably the hub for binding multiple enzymes to the interior of the BMC; modeling suggests PduC, PduD, PduG and PduM are targeted to PduJ (Probable).<ref>PMID:12923081</ref> <ref>PMID:21239588</ref> <ref>PMID:24747050</ref> <ref>PMID:27561553</ref> <ref>PMID:33227310</ref> <ref>PMID:25646976</ref>   The 1,2-propanediol (1,2-PD) degradation 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:18296526</ref> <ref>PMID:28475631</ref>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
+[[Category: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]]
+[[Category: Chun S]]
+[[Category: Sawaya MR]]
+[[Category: Yeates TO]]

5d6v

From Proteopedia

Current revision

PduJ K25A mutant, from Salmonella enterica serovar Typhimurium LT2, PduJ mutant

Structural highlights

Function

References

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Proteopedia Page Contributors and Editors (what is this?)

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