PDUK_SALTY
ID PDUK_SALTY Reviewed; 160 AA.
AC Q9XDN6; Q7BV80;
DT 25-MAY-2022, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1999, sequence version 1.
DT 03-AUG-2022, entry version 86.
DE RecName: Full=Bacterial microcompartment shell protein PduK {ECO:0000303|PubMed:12923081};
DE AltName: Full=Propanediol utilization protein PduK;
GN Name=pduK {ECO:0000303|PubMed:10498708}; OrderedLocusNames=STM2046;
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 IDENTIFICATION BY MASS SPECTROMETRY, 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 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 [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 POSSIBLE COFACTOR.
RX PubMed=20870711; DOI=10.1074/jbc.m110.160580;
RA Crowley C.S., Cascio D., Sawaya M.R., Kopstein J.S., Bobik T.A.,
RA Yeates T.O.;
RT "Structural insight into the mechanisms of transport across the Salmonella
RT enterica Pdu microcompartment shell.";
RL J. Biol. Chem. 285:37838-37846(2010).
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 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).
CC -!- FUNCTION: A minor shell protein of the bacterial microcompartment (BMC)
CC dedicated to 1,2-propanediol (1,2-PD) degradation. The isolated BMC
CC shell component protein ratio for J:A:B':B:K:T:U is approximately
CC 15:10:7:6:1:1:2 (PubMed:12923081). Not required for structural
CC integrity of BMCs nor to mitigate propionaldehyde toxicity, it might be
CC involved in spatial organization of BMCs (PubMed:21239588).
CC {ECO:0000269|PubMed:12923081, ECO:0000269|PubMed:21239588}.
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:0000269|PubMed:18296526, ECO:0000305|PubMed:28475631}.
CC -!- COFACTOR:
CC Name=Fe cation; Xref=ChEBI:CHEBI:24875;
CC Evidence={ECO:0000269|PubMed:20870711};
CC Note=The C-terminal 70 residues (positions 90-160) when overexpressed
CC in E.coli bind Fe (PubMed:20870711). Might bind an [Fe-S] cluster in
CC vivo (Probable). {ECO:0000269|PubMed:20870711,
CC ECO:0000305|PubMed:20870711};
CC -!- PATHWAY: Polyol metabolism; 1,2-propanediol degradation.
CC {ECO:0000305|PubMed:10498708}.
CC -!- SUBUNIT: Interacts with shell proteins PduA and PduP and assembly
CC protein PduM. {ECO:0000250|UniProtKB:B1VB70}.
CC -!- SUBCELLULAR LOCATION: Bacterial microcompartment
CC {ECO:0000269|PubMed:12923081}.
CC -!- INDUCTION: BMC production is induced by growth on 1,2-PD vitamin B12
CC medium. {ECO:0000269|PubMed:10498708}.
CC -!- DISRUPTION PHENOTYPE: Releases increased amounts of acetaldehyde when
CC grown on propanediol (PubMed:16585748). Half the cells seem to form BMC
CC aggregates with visible shells, the other half have no BMCs. Grows
CC normally on 1,2-PD and vitamin B12 (PubMed:21239588). A double pduJ-
CC pduK strain grows in an interrupted manner on 1,2-PD and vitamin B12;
CC grows for a while then stops, then restarts as toxic propionaldehyde
CC accumulates and then decreases (PubMed:18296526).
CC {ECO:0000269|PubMed:16585748, ECO:0000269|PubMed:18296526,
CC 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 -!- 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}.
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DR EMBL; AF026270; AAD39010.1; -; Genomic_DNA.
DR EMBL; AE006468; AAL20950.1; -; Genomic_DNA.
DR RefSeq; NP_460991.3; NC_003197.2.
DR RefSeq; WP_001284390.1; NC_003197.2.
DR AlphaFoldDB; Q9XDN6; -.
DR SMR; Q9XDN6; -.
DR STRING; 99287.STM2046; -.
DR PaxDb; Q9XDN6; -.
DR EnsemblBacteria; AAL20950; AAL20950; STM2046.
DR GeneID; 1253567; -.
DR KEGG; stm:STM2046; -.
DR HOGENOM; CLU_064903_3_3_6; -.
DR PhylomeDB; Q9XDN6; -.
DR BioCyc; SENT99287:STM2046-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; 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; PS51930; BMC_2; 1.
PE 1: Evidence at protein level;
KW Bacterial microcompartment; Iron; Reference proteome.
FT CHAIN 1..160
FT /note="Bacterial microcompartment shell protein PduK"
FT /id="PRO_0000454254"
FT DOMAIN 11..96
FT /note="BMC"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01278"
SQ SEQUENCE 160 AA; 16806 MW; F7A741B4248C26D6 CRC64;
MANKEHRVKQ SLGLLEVCGL ALAISCADIM AKSASITLLA LEKTNGSGWM VIKITGDVAS
VQAAITTGAH FAEQWNGLVA HKVIARPGEG ILLAETPSPS VIEPEPEASE IADVVSEAPA
EEAPQESELV SCNLCLDPKC PRQKGEPRTL CIHSGKRGEA
