PDUJ_SALTY
ID PDUJ_SALTY Reviewed; 91 AA.
AC H9L478;
DT 25-MAY-2022, integrated into UniProtKB/Swiss-Prot.
DT 16-MAY-2012, sequence version 1.
DT 03-AUG-2022, entry version 56.
DE RecName: Full=Bacterial microcompartment shell protein PduJ {ECO:0000303|PubMed:12923081};
DE AltName: Full=Bacterial microcompartment protein homohexamer {ECO:0000305};
DE Short=BMC-H {ECO:0000303|PubMed:33227310};
DE AltName: Full=Propanediol utilization protein PduJ;
GN Name=pduJ {ECO:0000303|PubMed:10498708}; OrderedLocusNames=STM2045;
OS Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Salmonella.
OX NCBI_TaxID=99287;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], PATHWAY, AND INDUCTION.
RC STRAIN=LT2;
RX PubMed=10498708; DOI=10.1128/jb.181.19.5967-5975.1999;
RA Bobik T.A., Havemann G.D., Busch R.J., Williams D.S., Aldrich H.C.;
RT "The propanediol utilization (pdu) operon of Salmonella enterica serovar
RT typhimurium LT2 includes genes necessary for formation of polyhedral
RT organelles involved in coenzyme B(12)-dependent 1, 2-propanediol
RT degradation.";
RL J. Bacteriol. 181:5967-5975(1999).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=LT2 / SGSC1412 / ATCC 700720;
RX PubMed=11677609; DOI=10.1038/35101614;
RA McClelland M., Sanderson K.E., Spieth J., Clifton S.W., Latreille P.,
RA Courtney L., Porwollik S., Ali J., Dante M., Du F., Hou S., Layman D.,
RA Leonard S., Nguyen C., Scott K., Holmes A., Grewal N., Mulvaney E.,
RA Ryan E., Sun H., Florea L., Miller W., Stoneking T., Nhan M., Waterston R.,
RA Wilson R.K.;
RT "Complete genome sequence of Salmonella enterica serovar Typhimurium LT2.";
RL Nature 413:852-856(2001).
RN [3]
RP PROTEIN SEQUENCE OF 1-7, FUNCTION, AND SUBCELLULAR LOCATION.
RC STRAIN=LT2;
RX PubMed=12923081; DOI=10.1128/jb.185.17.5086-5095.2003;
RA Havemann G.D., Bobik T.A.;
RT "Protein content of polyhedral organelles involved in coenzyme B12-
RT dependent degradation of 1,2-propanediol in Salmonella enterica serovar
RT Typhimurium LT2.";
RL J. Bacteriol. 185:5086-5095(2003).
RN [4]
RP DISRUPTION PHENOTYPE.
RC STRAIN=LT2;
RX PubMed=9023178; DOI=10.1128/jb.179.4.1013-1022.1997;
RA Walter D., Ailion M., Roth J.;
RT "Genetic characterization of the pdu operon: use of 1,2-propanediol in
RT Salmonella typhimurium.";
RL J. Bacteriol. 179:1013-1022(1997).
RN [5]
RP DISRUPTION PHENOTYPE.
RC STRAIN=LT2;
RX PubMed=18296526; DOI=10.1128/jb.01925-07;
RA Sampson E.M., Bobik T.A.;
RT "Microcompartments for B12-dependent 1,2-propanediol degradation provide
RT protection from DNA and cellular damage by a reactive metabolic
RT intermediate.";
RL J. Bacteriol. 190:2966-2971(2008).
RN [6]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=LT2;
RX PubMed=21239588; DOI=10.1128/jb.01473-10;
RA Cheng S., Sinha S., Fan C., Liu Y., Bobik T.A.;
RT "Genetic analysis of the protein shell of the microcompartments involved in
RT coenzyme B12-dependent 1,2-propanediol degradation by Salmonella.";
RL J. Bacteriol. 193:1385-1392(2011).
RN [7]
RP INTERACTION WITH PDUP.
RC STRAIN=LT2;
RX PubMed=22927404; DOI=10.1073/pnas.1207516109;
RA Fan C., Cheng S., Sinha S., Bobik T.A.;
RT "Interactions between the termini of lumen enzymes and shell proteins
RT mediate enzyme encapsulation into bacterial microcompartments.";
RL Proc. Natl. Acad. Sci. U.S.A. 109:14995-15000(2012).
RN [8]
RP BIOTECHNOLOGY (ARTIFICIAL BMCS).
RC STRAIN=LT2;
RX PubMed=24014666; DOI=10.1099/mic.0.069922-0;
RA Sargent F., Davidson F.A., Kelly C.L., Binny R., Christodoulides N.,
RA Gibson D., Johansson E., Kozyrska K., Lado L.L., MacCallum J., Montague R.,
RA Ortmann B., Owen R., Coulthurst S.J., Dupuy L., Prescott A.R., Palmer T.;
RT "A synthetic system for expression of components of a bacterial
RT microcompartment.";
RL Microbiology 159:2427-2436(2013).
RN [9]
RP FUNCTION, SUBCELLULAR LOCATION, DISRUPTION PHENOTYPE, AND MUTAGENESIS OF
RP LYS-25.
RC STRAIN=LT2;
RX PubMed=24747050; DOI=10.1016/j.jmb.2014.04.012;
RA Sinha S., Cheng S., Sung Y.W., McNamara D.E., Sawaya M.R., Yeates T.O.,
RA Bobik T.A.;
RT "Alanine scanning mutagenesis identifies an asparagine-arginine-lysine
RT triad essential to assembly of the shell of the Pdu microcompartment.";
RL J. Mol. Biol. 426:2328-2345(2014).
RN [10]
RP MODELING OF BMCS, AND FUNCTION.
RX PubMed=25646976; DOI=10.1371/journal.pcbi.1004067;
RA Jorda J., Liu Y., Bobik T.A., Yeates T.O.;
RT "Exploring bacterial organelle interactomes: a model of the protein-protein
RT interaction network in the Pdu microcompartment.";
RL PLoS Comput. Biol. 11:e1004067-e1004067(2015).
RN [11]
RP SYSTEM-MODELING, AND FUNCTION.
RC STRAIN=LT2;
RX PubMed=28475631; DOI=10.1371/journal.pcbi.1005525;
RA Jakobson C.M., Tullman-Ercek D., Slininger M.F., Mangan N.M.;
RT "A systems-level model reveals that 1,2-Propanediol utilization
RT microcompartments enhance pathway flux through intermediate
RT sequestration.";
RL PLoS Comput. Biol. 13:e1005525-e1005525(2017).
RN [12]
RP FUNCTION, DISRUPTION PHENOTYPE, AND MUTAGENESIS OF LYS-25.
RC STRAIN=LT2;
RX PubMed=33227310; DOI=10.1016/j.jmb.2020.11.020;
RA Kennedy N.W., Ikonomova S.P., Slininger Lee M., Raeder H.W.,
RA Tullman-Ercek D.;
RT "Self-assembling Shell Proteins PduA and PduJ have Essential and Redundant
RT Roles in Bacterial Microcompartment Assembly.";
RL J. Mol. Biol. 433:166721-166721(2021).
RN [13] {ECO:0007744|PDB:5D6V}
RP X-RAY CRYSTALLOGRAPHY (1.50 ANGSTROMS) OF 2-91, FUNCTION, SUBUNIT,
RP DISRUPTION PHENOTYPE, AND MUTAGENESIS OF LYS-25 AND SER-39.
RC STRAIN=LT2;
RX PubMed=27561553; DOI=10.1111/mmi.13423;
RA Chowdhury C., Chun S., Sawaya M.R., Yeates T.O., Bobik T.A.;
RT "The function of the PduJ microcompartment shell protein is determined by
RT the genomic position of its encoding gene.";
RL Mol. Microbiol. 101:770-783(2016).
CC -!- FUNCTION: One of the major shell proteins of the bacterial
CC microcompartment (BMC) dedicated to 1,2-propanediol (1,2-PD)
CC degradation. The isolated BMC shell component protein ratio for
CC J:A:B':B:K:T:U is approximately 15:10:7:6:1:1:2 (PubMed:12923081). At
CC least one of PduA or PduJ is required for BMC assembly; it must be
CC encoded as the first gene in the pdu operon (PubMed:33227310,
CC PubMed:27561553). Required for structural integrity of BMCs and to
CC mitigate propionaldehyde toxicity, probably joins facets responsible
CC for BMC closure (PubMed:21239588). Edge residues (particularly Lys-25)
CC are important for function and assembly of the BMC (PubMed:24747050).
CC 80% identical to PduA; although their pore regions appear structurally
CC identical, unlike PduA plays no role in 1,2-PD diffusion into or out of
CC the BMC shell. If pduJ is cloned in the chromosomal position of pduA it
CC is able to complement a pduA deletion; it then has a functional pore as
CC it assumes the transport functions of PduA (PubMed:27561553).
CC Overexpression of this protein leads to aberrant filaments that extend
CC the length of the cell, cross the cleavage furrow and impair division.
CC The filaments form nanotubes with a hollow center (PubMed:33227310).
CC Modeling suggests PduJ is probably the hub for binding multiple enzymes
CC to the interior of the BMC; modeling suggests PduC, PduD, PduG and PduM
CC are targeted to PduJ (Probable). {ECO:0000269|PubMed:12923081,
CC ECO:0000269|PubMed:21239588, ECO:0000269|PubMed:24747050,
CC ECO:0000269|PubMed:27561553, ECO:0000269|PubMed:33227310,
CC ECO:0000305|PubMed:25646976}.
CC -!- FUNCTION: The 1,2-propanediol (1,2-PD) degradation bacterial
CC microcompartment (BMC) concentrates low levels of 1,2-PD catabolic
CC enzymes, concentrates volatile reaction intermediates thus enhancing
CC pathway flux and keeps the level of toxic, mutagenic propionaldehyde
CC low. {ECO:0000269|PubMed:18296526, ECO:0000305|PubMed:28475631}.
CC -!- PATHWAY: Polyol metabolism; 1,2-propanediol degradation.
CC {ECO:0000305|PubMed:10498708}.
CC -!- SUBUNIT: Homohexamer with a central pore of about 5.7 Angstroms in
CC diameter (PubMed:27561553). Interacts with PduP, which targets PduP to
CC the BMC (PubMed:22927404). {ECO:0000269|PubMed:22927404,
CC ECO:0000269|PubMed:27561553}.
CC -!- SUBCELLULAR LOCATION: Bacterial microcompartment
CC {ECO:0000269|PubMed:12923081, ECO:0000269|PubMed:24747050}.
CC -!- INDUCTION: BMC production is induced by growth on 1,2-PD vitamin B12
CC medium. {ECO:0000269|PubMed:10498708}.
CC -!- DISRUPTION PHENOTYPE: Cells lacking this gene are defective in aerobic
CC degradation of propanediol (PubMed:9023178). Most cells lack BMCs, 22%
CC have highly elongated internal structures, 20% have amorphous polar
CC bodies. Grows in an interrupted manner on 1,2-PD and vitamin B12; grows
CC for a while then stops, then restarts as if a toxic compound was
CC accumulating and then decreases (PubMed:21239588). Grows faster under
CC limiting vitamin B12 conditions, forms elongated BMCs
CC (PubMed:24747050). A double pduJ-pduK strain grows in an interrupted
CC manner on 1,2-PD and vitamin B12; grows for a while then stops, then
CC restarts as toxic propionaldehyde accumulates and then decreases
CC (PubMed:18296526). Makes elongated BMCs; this phenotype can be rescued
CC by PduA or PduJ, but PduJ encoded on a plasmid cannot rescue a PduA
CC deletion. When pduJ is cloned in the chromosomal position of pduA it
CC substantially rescues the pduA deletion (PubMed:27561553,
CC PubMed:33227310). Single pduA deletion makes BMCs but a double pduA-
CC pduJ deletion does not (PubMed:33227310). {ECO:0000269|PubMed:18296526,
CC ECO:0000269|PubMed:21239588, ECO:0000269|PubMed:24747050,
CC ECO:0000269|PubMed:27561553, ECO:0000269|PubMed:33227310,
CC ECO:0000269|PubMed:9023178}.
CC -!- BIOTECHNOLOGY: Artificial BMCs can be made in E.coli by expressing
CC pduA-pduB/B'-pduT-pduU-pduN-pduJ-pduK (in this order). Enzymes can be
CC targeted to the BMC, and appear to be encapsulated within it.
CC {ECO:0000269|PubMed:24014666}.
CC -!- MISCELLANEOUS: Bacterial microcompartments (BMC) 100-200 nm in cross
CC section are formed during aerobic growth on minimal 1,2-PD-B12 or
CC anaerobic growth on 1,2-PD-tetrathionate medium, but not during aerobic
CC growth on glucose, anerobic growth on glucose or pyruvate-tetrathionate
CC (PubMed:10498708). BMCs can constitute up to 10% of total cell protein
CC (PubMed:12923081). {ECO:0000269|PubMed:10498708,
CC ECO:0000269|PubMed:12923081}.
CC -!- SIMILARITY: Belongs to the bacterial microcompartments protein family.
CC {ECO:0000255|PROSITE-ProRule:PRU01278}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; AF026270; AAD39009.1; -; Genomic_DNA.
DR EMBL; AE006468; AAL20949.1; -; Genomic_DNA.
DR RefSeq; NP_460990.1; NC_003197.2.
DR RefSeq; WP_001057755.1; NC_003197.2.
DR PDB; 5D6V; X-ray; 1.50 A; A=2-91.
DR PDBsum; 5D6V; -.
DR AlphaFoldDB; H9L478; -.
DR SMR; H9L478; -.
DR STRING; 99287.STM2045; -.
DR PaxDb; H9L478; -.
DR EnsemblBacteria; AAL20949; AAL20949; STM2045.
DR GeneID; 1253566; -.
DR GeneID; 61287921; -.
DR GeneID; 64335886; -.
DR GeneID; 66587161; -.
DR KEGG; stm:STM2045; -.
DR PATRIC; fig|99287.12.peg.2167; -.
DR HOGENOM; CLU_064903_5_3_6; -.
DR OMA; ESWVIIP; -.
DR PhylomeDB; H9L478; -.
DR BioCyc; SENT99287:STM2045-MON; -.
DR UniPathway; UPA00621; -.
DR Proteomes; UP000001014; Chromosome.
DR GO; GO:0031472; C:propanediol degradation polyhedral organelle; IDA:UniProtKB.
DR GO; GO:0051144; P:propanediol catabolic process; IEA:UniProtKB-UniPathway.
DR Gene3D; 3.30.70.1710; -; 1.
DR InterPro; IPR020808; Bact_microcomp_CS.
DR InterPro; IPR000249; BMC_dom.
DR InterPro; IPR037233; CcmK-like_sf.
DR InterPro; IPR044872; CcmK/CsoS1_BMC.
DR Pfam; PF00936; BMC; 1.
DR SMART; SM00877; BMC; 1.
DR SUPFAM; SSF143414; SSF143414; 1.
DR PROSITE; PS01139; BMC_1; 1.
DR PROSITE; PS51930; BMC_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Bacterial microcompartment; Direct protein sequencing;
KW Reference proteome; Transport.
FT CHAIN 1..91
FT /note="Bacterial microcompartment shell protein PduJ"
FT /id="PRO_0000454252"
FT DOMAIN 4..88
FT /note="BMC"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01278"
FT MUTAGEN 25
FT /note="K->A: Produces amorphous bodies instead of BMCs.
FT Reduces crystallographic problems that result from edge-to-
FT edge aggregation of BMC hexamers. No longer forms filaments
FT upon overexpression, does not restore BMC formation to a
FT double pduA-pduJ deletion."
FT /evidence="ECO:0000269|PubMed:24747050,
FT ECO:0000269|PubMed:27561553, ECO:0000269|PubMed:33227310"
FT MUTAGEN 39
FT /note="S->L: Wild-type growth rate, BMCs appear normal,
FT wild-type DDH activity. In the chromosomal position of
FT pduA, less permeable to 1,2-PD, 65% DDH activity, cells
FT grow slower on 1,2-PD."
FT /evidence="ECO:0000269|PubMed:27561553"
SQ SEQUENCE 91 AA; 9068 MW; A02F8FD887AF22DF CRC64;
MNNALGLVET KGLVGAIEAA DAMVKSANVQ LVGYEKIGSG LVTVMVRGDV GAVKAAVDAG
SAAASVVGEV KSCHVIPRPH SDVEAILPKS A
