PDUT_SALTY
ID PDUT_SALTY Reviewed; 184 AA.
AC Q9XDM8; Q7BV73;
DT 25-MAY-2022, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1999, sequence version 1.
DT 03-AUG-2022, entry version 101.
DE RecName: Full=Bacterial microcompartment shell protein PduT {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 PduT;
GN Name=pduT {ECO:0000303|PubMed:10498708}; OrderedLocusNames=STM2054;
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=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 [5]
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 [6]
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 [7]
RP FUNCTION, DISRUPTION PHENOTYPE, BIOTECHNOLOGY (ALTERED BMC PERMEABILITY),
RP AND MUTAGENESIS OF CYS-38.
RC STRAIN=LT2;
RX PubMed=31674899; DOI=10.1099/mic.0.000872;
RA Chowdhury C., Bobik T.A.;
RT "Engineering the PduT shell protein to modify the permeability of the 1,2-
RT propanediol microcompartment of Salmonella.";
RL Microbiology 165:1355-1364(2019).
RN [8] {ECO:0007744|PDB:3N79}
RP X-RAY CRYSTALLOGRAPHY (1.50 ANGSTROMS), FUNCTION, PROBABLE COFACTOR,
RP SUBUNIT, AND MUTAGENESIS OF CYS-38.
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 [9] {ECO:0007744|PDB:3VCD, ECO:0007744|PDB:4DDF}
RP X-RAY CRYSTALLOGRAPHY (2.35 ANGSTROMS), SUBUNIT, AND BIOTECHNOLOGY
RP (SELF-ASSEMBLY).
RX PubMed=22654060; DOI=10.1126/science.1219364;
RA King N.P., Sheffler W., Sawaya M.R., Vollmar B.S., Sumida J.P., Andre I.,
RA Gonen T., Yeates T.O., Baker D.;
RT "Computational design of self-assembling protein nanomaterials with atomic
RT level accuracy.";
RL Science 336:1171-1174(2012).
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, may
CC selectively transport specific metabolites (PubMed:21239588). May be
CC involved in electron transport across the BMC shell (Probable). Can be
CC engineered to alter permeability of the BMC shell (PubMed:31674899).
CC {ECO:0000269|PubMed:12923081, ECO:0000269|PubMed:21239588,
CC ECO:0000269|PubMed:31674899, ECO:0000305|PubMed:20870711}.
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 -!- COFACTOR:
CC Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
CC Evidence={ECO:0000250|UniProtKB:P0DUM6, ECO:0000305|PubMed:20870711};
CC Note=Probably bound by a single Cys residue from each subunit; which
CC protein provides the fourth ligand is unknown.
CC {ECO:0000305|PubMed:20870711};
CC -!- PATHWAY: Polyol metabolism; 1,2-propanediol degradation.
CC {ECO:0000305|PubMed:10498708}.
CC -!- SUBUNIT: Homotrimerizes to form a pseudohexamer; in wild-type the
CC central triangular pore is probably blocked by the [4Fe-4S] center
CC (PubMed:20870711, PubMed:22654060). Interacts with PduS (By
CC similarity). {ECO:0000250|UniProtKB:P0DUV7,
CC ECO:0000269|PubMed:20870711, ECO:0000269|PubMed:22654060}.
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: No visible effect on BMC morphology. Slight
CC growth impairment on 1,2-propanediol and vitamin B12.
CC {ECO:0000269|PubMed:21239588, ECO:0000269|PubMed:31674899}.
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: When mutated at 9 positions (construct O3-33 with these
CC mutations; K15A, M67L, N148A, N149L, E156S, E160A, K161Y, R167A, V169L)
CC self-assembles into bodies with 24 subunits, suitable for
CC nanotechnology uses. {ECO:0000269|PubMed:22654060,
CC ECO:0007744|PDB:3VCD, ECO:0007744|PDB:4DDF}.
CC -!- BIOTECHNOLOGY: Removal of the [4Fe-4S] center by mutagenesis and
CC different substitutions of Cys-38 allows an increased growth rate under
CC certain limiting-conditions ('L-40' in PduA, pduQ deletion), strongly
CC suggesting this subunit has acquired the ability to transport 1,2-PD,
CC propionaldehyde and NAD(+)/NADH across the BMC shell.
CC {ECO:0000269|PubMed:31674899}.
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; AAD39018.1; -; Genomic_DNA.
DR EMBL; AE006468; AAL20958.1; -; Genomic_DNA.
DR RefSeq; NP_460999.1; NC_003197.2.
DR RefSeq; WP_000075772.1; NC_003197.2.
DR PDB; 3N79; X-ray; 1.50 A; A=1-184.
DR PDB; 3VCD; X-ray; 2.35 A; A/B/C/D/E/F/G/H=1-184.
DR PDB; 4DDF; X-ray; 3.15 A; A/B/C/D/E/F/G/H/I/J/K/L=1-184.
DR PDBsum; 3N79; -.
DR PDBsum; 3VCD; -.
DR PDBsum; 4DDF; -.
DR AlphaFoldDB; Q9XDM8; -.
DR SMR; Q9XDM8; -.
DR STRING; 99287.STM2054; -.
DR PaxDb; Q9XDM8; -.
DR EnsemblBacteria; AAL20958; AAL20958; STM2054.
DR GeneID; 1253575; -.
DR KEGG; stm:STM2054; -.
DR PATRIC; fig|99287.12.peg.2176; -.
DR HOGENOM; CLU_115793_0_0_6; -.
DR OMA; VVETWSV; -.
DR PhylomeDB; Q9XDM8; -.
DR BioCyc; SENT99287:STM2054-MON; -.
DR UniPathway; UPA00621; -.
DR Proteomes; UP000001014; Chromosome.
DR GO; GO:0031472; C:propanediol degradation polyhedral organelle; IDA:UniProtKB.
DR GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0051144; P:propanediol catabolic process; IEA:UniProtKB-UniPathway.
DR Gene3D; 3.30.70.1710; -; 2.
DR InterPro; IPR000249; BMC_dom.
DR InterPro; IPR037233; CcmK-like_sf.
DR InterPro; IPR044872; CcmK/CsoS1_BMC.
DR InterPro; IPR011238; Organelle_shell_prot_PduT.
DR Pfam; PF00936; BMC; 2.
DR PIRSF; PIRSF034834; PduT; 1.
DR SMART; SM00877; BMC; 2.
DR SUPFAM; SSF143414; SSF143414; 2.
DR PROSITE; PS51930; BMC_2; 2.
PE 1: Evidence at protein level;
KW 3D-structure; 4Fe-4S; Bacterial microcompartment; Iron; Iron-sulfur;
KW Metal-binding; Reference proteome; Transport.
FT CHAIN 1..184
FT /note="Bacterial microcompartment shell protein PduT"
FT /id="PRO_0000454256"
FT DOMAIN 4..86
FT /note="BMC 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01278"
FT DOMAIN 96..182
FT /note="BMC 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01278"
FT BINDING 38
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000305|PubMed:20870711"
FT MUTAGEN 38
FT /note="C->A: Allows movement of 1,2-PD and NAD(+)/NADH
FT across the BMC, excretes slightly more propionaldehyde,
FT makes normal BMCs."
FT /evidence="ECO:0000269|PubMed:31674899"
FT MUTAGEN 38
FT /note="C->I: No transport of 1,2-PD or NAD(+)/NADH across
FT the BMC, no change in propionaldehyde excretion, makes
FT normal BMCs."
FT /evidence="ECO:0000269|PubMed:31674899"
FT MUTAGEN 38
FT /note="C->S: Purified protein is more stable, crystallized,
FT has a triangular pore of about 46 Angstroms(2) area. Allows
FT movement of 1,2-PD and NAD(+)/NADH across the BMC, excretes
FT slightly more propionaldehyde, makes normal BMCs."
FT /evidence="ECO:0000269|PubMed:20870711,
FT ECO:0000269|PubMed:31674899, ECO:0007744|PDB:3N79"
FT MUTAGEN 38
FT /note="C->W: No transport of 1,2-PD or NAD(+)/NADH across
FT the BMC, makes normal BMCs."
FT /evidence="ECO:0000269|PubMed:31674899"
SQ SEQUENCE 184 AA; 19150 MW; A738E27F5E0ED7A3 CRC64;
MSQAIGILEL TSIAKGMELG DAMLKSANVD LLVSKTICPG KFLLMLGGDI GAIQQAIETG
TSQAGEMLVD SLVLANIHPS VLPAISGLNS VDKRQAVGIV ETWSVAACIS AADRAVKGSN
VTLVRVHMAF GIGGKCYMVV AGDVSDVNNA VTVASESAGE KGLLVYRSVI PRPHEAMWRQ
MVEG
