PDUB_SALTY
ID PDUB_SALTY Reviewed; 270 AA.
AC P37449;
DT 01-OCT-1994, integrated into UniProtKB/Swiss-Prot.
DT 23-FEB-2022, sequence version 3.
DT 03-AUG-2022, entry version 102.
DE RecName: Full=Bacterial microcompartment shell protein PduB {ECO:0000303|PubMed:12923081};
DE AltName: Full=Bacterial microcompartment protein homotrimer {ECO:0000305};
DE Short=BMC-T {ECO:0000305};
DE AltName: Full=Propanediol utilization protein PduB;
GN Name=pduB {ECO:0000303|PubMed:8071226}; OrderedLocusNames=STM2039;
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].
RC STRAIN=LT2;
RX PubMed=8071226; DOI=10.1128/jb.176.17.5474-5482.1994;
RA Chen P., Anderson D.I., Roth J.R.;
RT "The control region of the pdu/cob regulon in Salmonella typhimurium.";
RL J. Bacteriol. 176:5474-5482(1994).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=LT2;
RX PubMed=9352910; DOI=10.1128/jb.179.21.6633-6639.1997;
RA Bobik T.A., Xu Y., Jeter R.M., Otto K.E., Roth J.R.;
RT "Propanediol utilization genes (pdu) of Salmonella typhimurium: three genes
RT for the propanediol dehydratase.";
RL J. Bacteriol. 179:6633-6639(1997).
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], PATHWAY, INDUCTION, AND DISRUPTION
RP PHENOTYPE.
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 [4]
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 [5]
RP PROTEIN SEQUENCE OF 2-8 AND 39-45, FUNCTION, PDUB AND PDUB' ISOFORMS, AND
RP 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 [6]
RP DISRUPTION PHENOTYPE.
RC STRAIN=LT2;
RX PubMed=11844753; DOI=10.1128/jb.184.5.1253-1261.2002;
RA Havemann G.D., Sampson E.M., Bobik T.A.;
RT "PduA is a shell protein of polyhedral organelles involved in coenzyme
RT B(12)-dependent degradation of 1,2-propanediol in Salmonella enterica
RT serovar typhimurium LT2.";
RL J. Bacteriol. 184:1253-1261(2002).
RN [7]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=LT2;
RX PubMed=16585748; DOI=10.1128/jb.188.8.2865-2874.2006;
RA Penrod J.T., Roth J.R.;
RT "Conserving a volatile metabolite: a role for carboxysome-like organelles
RT in Salmonella enterica.";
RL J. Bacteriol. 188:2865-2874(2006).
RN [8]
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 [9]
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 [10]
RP SUBCELLULAR LOCATION, AND 2 ISOFORMS.
RC STRAIN=LT2;
RX PubMed=27063436; DOI=10.1038/srep24359;
RA Held M., Kolb A., Perdue S., Hsu S.Y., Bloch S.E., Quin M.B.,
RA Schmidt-Dannert C.;
RT "Engineering formation of multiple recombinant Eut protein nanocompartments
RT in E. coli.";
RL Sci. Rep. 6:24359-24359(2016).
RN [11]
RP FUNCTION, DOMAIN, AND MUTAGENESIS OF 1-MET--ALA-37; 6-LEU--ALA-12; VAL-7;
RP ILE-10; 11-MET--ALA-25; MET-11; VAL-14; 27-PRO--PRO-32 AND MET-38.
RC STRAIN=LT2;
RX PubMed=28138097; DOI=10.1128/jb.00785-16;
RA Lehman B.P., Chowdhury C., Bobik T.A.;
RT "The N Terminus of the PduB Protein Binds the Protein Shell of the Pdu
RT Microcompartment to Its Enzymatic Core.";
RL J. Bacteriol. 199:0-0(2017).
RN [12]
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 [13]
RP BIOTECHNOLOGY (FORMING PROTEIN SHELLS).
RC STRAIN=LT2;
RX PubMed=31845931; DOI=10.1039/c9tb02224d;
RA Bari N.K., Kumar G., Hazra J.P., Kaur S., Sinha S.;
RT "Functional protein shells fabricated from the self-assembling protein
RT sheets of prokaryotic organelles.";
RL J. Mater. Chem. B 8:523-533(2020).
CC -!- FUNCTION: The two proteins produced are among the major shell proteins
CC of the bacterial microcompartment (BMC) dedicated to 1,2-propanediol
CC (1,2-PD) degradation (PubMed:12923081, PubMed:21239588). Required for
CC structural integrity of BMCs and to mitigate propionaldehyde toxicity
CC (PubMed:21239588). The N-terminal 13 residues are important for correct
CC assembly of the BMC shell (PubMed:28138097). The isolated BMC shell
CC component protein ratio for J:A:B':B:K:T:U is approximately
CC 15:10:7:6:1:1:2 (PubMed:12923081). The N-terminus of the long form
CC (PduB) is required for correct formation of BMCs, deletions in the
CC first 37 residues have substantially reduced levels of the major lumen
CC enzymes. May play a major role in binding the enzyme contents to the
CC shell (PubMed:28138097). {ECO:0000269|PubMed:12923081,
CC ECO:0000269|PubMed:21239588, ECO:0000269|PubMed:28138097}.
CC -!- FUNCTION: The 1,2-PD-specific bacterial microcompartment (BMC)
CC concentrates low levels of 1,2-PD catabolic enzymes, concentrates
CC volatile reaction intermediates thus enhancing pathway flux and keeps
CC the level of toxic, mutagenic propionaldehyde low.
CC {ECO:0000305|PubMed:28475631}.
CC -!- PATHWAY: Polyol metabolism; 1,2-propanediol degradation.
CC {ECO:0000305|PubMed:10498708}.
CC -!- SUBUNIT: Homotrimerizes to form a pseudohexamer with a central pore.
CC The trimers pack into an array. {ECO:0000250|UniProtKB:A5VMB3}.
CC -!- SUBCELLULAR LOCATION: Bacterial microcompartment
CC {ECO:0000269|PubMed:12923081, ECO:0000269|PubMed:27063436}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative promoter usage; Named isoforms=2;
CC Comment=A Shine-Dalgarno sequence and an appropriate start codon
CC precede each protein product (Probable). Mutation of Met-38 prevents
CC translation of PduB' in vivo (PubMed:28138097).
CC {ECO:0000269|PubMed:28138097, ECO:0000305|PubMed:12923081};
CC Name=PduB;
CC IsoId=P37449-1; Sequence=Displayed;
CC Name=PduB';
CC IsoId=P37449-2; Sequence=VSP_061270;
CC -!- INDUCTION: BMC production is induced by growth on 1,2-PD vitamin B12
CC medium. {ECO:0000269|PubMed:10498708}.
CC -!- DOMAIN: A probable alpha helix (residues 6-18) probably binds to cargo
CC enzymes, attaching them to the shell. {ECO:0000305|PubMed:28138097}.
CC -!- DOMAIN: Has 2 BMC domains which can evolve independently of each other.
CC {ECO:0000305}.
CC -!- PTM: In purified BMCs seen as a 28.0 kDa and 25.0 kDa form, both of
CC which have been N-terminally sequenced and whose N-fMet is removed; the
CC smaller form is called PduB'. {ECO:0000269|PubMed:12923081,
CC ECO:0000269|PubMed:27063436}.
CC -!- DISRUPTION PHENOTYPE: Releases increased amounts of acetaldehyde when
CC grown on propanediol (PubMed:16585748). Cells do not make BMCs, diol
CC dehydratase is found in diffuse aggregates near the cell pole; it was
CC later found this a double pduA-pduBB' deletion (PubMed:11844753). A
CC deletion that prevents synthesis of both proteins makes no BMCs, about
CC 20% of cells form amorphous polar bodies. Grows in an interrupted
CC manner on 1,2-PD and vitamin B12; grows for a while then stops, then
CC restarts as if a toxic compound was accumulating and then decreases
CC (PubMed:21239588). {ECO:0000269|PubMed:11844753,
CC ECO:0000269|PubMed:16585748, ECO:0000269|PubMed:21239588}.
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 -!- BIOTECHNOLOGY: Upon overexpression of PduB or PduB' and mixing of the
CC resulting purified sheets with 2-ethyl-1-hexanol, will form closed
CC shells. Enzymes (tested with endogenous BMC enzyme DDH and the
CC peroxidase activity of cytC) can be encapsulated in the shells; the
CC enzyme is active in the shells. The shells are permeable to a variety
CC of compounds, showing they could be used to make protein based
CC synthetic bioreactors. {ECO:0000269|PubMed:31845931}.
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 EutL/PduB family. {ECO:0000255|PROSITE-
CC ProRule:PRU01279}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAB84106.1; Type=Frameshift; Evidence={ECO:0000305};
CC Sequence=AAL20943.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
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DR EMBL; AF026270; AAB84106.1; ALT_FRAME; Genomic_DNA.
DR EMBL; AE006468; AAL20943.1; ALT_INIT; Genomic_DNA.
DR RefSeq; NP_460984.3; NC_003197.2.
DR RefSeq; WP_012539884.1; NC_003197.2.
DR AlphaFoldDB; P37449; -.
DR SMR; P37449; -.
DR STRING; 99287.STM2039; -.
DR PaxDb; P37449; -.
DR PRIDE; P37449; -.
DR DNASU; 1253560; -.
DR EnsemblBacteria; AAL20943; AAL20943; STM2039.
DR GeneID; 1253560; -.
DR KEGG; stm:STM2039; -.
DR HOGENOM; CLU_076302_0_0_6; -.
DR PhylomeDB; P37449; -.
DR BioCyc; SENT99287:STM2039-MON; -.
DR UniPathway; UPA00621; -.
DR Proteomes; UP000001014; Chromosome.
DR GO; GO:0031472; C:propanediol degradation polyhedral organelle; IDA:UniProtKB.
DR GO; GO:0005198; F:structural molecule activity; IEA:InterPro.
DR GO; GO:0051144; P:propanediol catabolic process; IEA:UniProtKB-UniPathway.
DR Gene3D; 3.30.70.1710; -; 2.
DR InterPro; IPR044870; BMC_CP.
DR InterPro; IPR000249; BMC_dom.
DR InterPro; IPR037233; CcmK-like_sf.
DR InterPro; IPR009193; EutL_PduB.
DR InterPro; IPR030984; PduB.
DR Pfam; PF00936; BMC; 2.
DR PIRSF; PIRSF012290; EutL_PduB; 1.
DR SMART; SM00877; BMC; 2.
DR SUPFAM; SSF143414; SSF143414; 2.
DR TIGRFAMs; TIGR04501; microcomp_PduB; 1.
DR PROSITE; PS51931; BMC_CP; 2.
PE 1: Evidence at protein level;
KW Alternative promoter usage; Bacterial microcompartment;
KW Direct protein sequencing; Reference proteome.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:12923081"
FT CHAIN 2..270
FT /note="Bacterial microcompartment shell protein PduB"
FT /id="PRO_0000201519"
FT DOMAIN 47..152
FT /note="BMC circularly permuted 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01279"
FT DOMAIN 154..258
FT /note="BMC circularly permuted 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01279"
FT REGION 6..18
FT /note="Probable helix that binds cargo to the BMC shell"
FT /evidence="ECO:0000305|PubMed:28138097"
FT VAR_SEQ 1..37
FT /note="Missing (in isoform PduB')"
FT /evidence="ECO:0000269|PubMed:12923081"
FT /id="VSP_061270"
FT MUTAGEN 1..37
FT /note="Missing: Makes large empty BMCs, makes about 11%
FT BMCs."
FT /evidence="ECO:0000269|PubMed:28138097"
FT MUTAGEN 6..12
FT /note="Missing: Makes large empty BMCs, makes about 30%
FT BMCs."
FT /evidence="ECO:0000269|PubMed:28138097"
FT MUTAGEN 7
FT /note="V->T: Makes about 80% BMCs, 78% diol dehydratase
FT content."
FT /evidence="ECO:0000269|PubMed:28138097"
FT MUTAGEN 10
FT /note="I->T: Makes about 25% BMCs, 35% diol dehydratase
FT content."
FT /evidence="ECO:0000269|PubMed:28138097"
FT MUTAGEN 11..25
FT /note="Missing: BMCs have a severe assembly defect, makes
FT about 27% BMCs."
FT /evidence="ECO:0000269|PubMed:28138097"
FT MUTAGEN 11
FT /note="M->S: Makes about 90% BMCs, 87% diol dehydratase
FT content."
FT /evidence="ECO:0000269|PubMed:28138097"
FT MUTAGEN 14
FT /note="V->T: Makes about 70% BMCs, 74% diol dehydratase
FT content."
FT /evidence="ECO:0000269|PubMed:28138097"
FT MUTAGEN 27..32
FT /note="Missing: Makes about 75% BMCs."
FT /evidence="ECO:0000269|PubMed:28138097"
FT MUTAGEN 38
FT /note="M->A: Does not make PduB', makes about 66% BMCs,
FT with wild-type appearance."
FT /evidence="ECO:0000269|PubMed:28138097"
FT CONFLICT 85
FT /note="G -> A (in Ref. 3; AAB84106)"
FT /evidence="ECO:0000305"
FT INIT_MET P37449-2:1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:12923081"
SQ SEQUENCE 270 AA; 28016 MW; A549ED606C6BAB5A CRC64;
MSSNELVEQI MAQVIARVAT PEQQAIPGQP QPIRETAMAE KSCSLTEFVG TAIGDTLGLV
IANVDTALLD AMKLEKRYRS IGILGARTGA GPHIMAADEA VKATNTEVVS IELPRDTKGG
AGHGSLIILG GNDVSDVKRG IEVALKELDR TFGDVYGNEA GHIELQYTAR ASYALEKAFG
APIGRACGII VGAPASVGVL MADTALKSAN VEVVAYSSPA HGTSFSNEAI LVISGDSGAV
RQAVTSAREI GKTVLATLGS EPKNDRPSYI
