PDUU_SALTY
ID PDUU_SALTY Reviewed; 116 AA.
AC P0A1D1; Q9XDM7;
DT 01-MAR-2005, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2005, sequence version 1.
DT 03-AUG-2022, entry version 76.
DE RecName: Full=Bacterial microcompartment shell protein PduU {ECO:0000303|PubMed:12923081};
DE AltName: Full=Bacterial microcompartment protein homohexamer {ECO:0000305};
DE Short=BMC-H {ECO:0000305};
DE AltName: Full=Propanediol utilization protein PduU;
GN Name=pduU {ECO:0000303|PubMed:10498708}; OrderedLocusNames=STM2055;
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 INTERACTION WITH PDUV, AND SUBCELLULAR LOCATION.
RC STRAIN=LT2;
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 [7]
RP SUBCELLULAR LOCATION.
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 [8]
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 [9] {ECO:0007744|PDB:3CGI}
RP X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS), SUBUNIT, AND DOMAIN.
RC STRAIN=LT2;
RX PubMed=18786396; DOI=10.1016/j.str.2008.05.013;
RA Crowley C.S., Sawaya M.R., Bobik T.A., Yeates T.O.;
RT "Structure of the PduU shell protein from the Pdu microcompartment of
RT Salmonella.";
RL Structure 16:1324-1332(2008).
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). Proteins
CC such as this one with circularly permuted BMC domains may play a key
CC role in conferring heterogeneity and flexibility in this BMC
CC (Probable). {ECO:0000269|PubMed:12923081, ECO:0000269|PubMed:21239588,
CC ECO:0000305}.
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: Homohexamer with a central pore lined by a beta-barrel.
CC Hexamers pack into a loose array (PubMed:18786396). Interacts with
CC PduV, probably via the beta-barrel which is predicted by modeling to be
CC on the exterior of the BMC (PubMed:25646976).
CC {ECO:0000269|PubMed:18786396, ECO:0000269|PubMed:25646976}.
CC -!- SUBCELLULAR LOCATION: Bacterial microcompartment
CC {ECO:0000269|PubMed:12923081, ECO:0000269|PubMed:27063436}. Note=The
CC N- and C-terminii are on the convex side of the hexamer, probably
CC inside the BMC (PubMed:18786396) (Probable). Modeling suggests the
CC beta-barrel is on the exterior of the BMC where it interacts with PduV
CC (Probable). {ECO:0000269|PubMed:18786396, ECO:0000305,
CC ECO:0000305|PubMed:25646976}.
CC -!- INDUCTION: BMC production is induced by growth on 1,2-PD vitamin B12
CC medium. {ECO:0000269|PubMed:10498708}.
CC -!- DOMAIN: One side of the hexamer is concave which is lined by
CC hydrophobic residues, the other side has a slightly protruding, 6-
CC stranded beta-barrel which is occluded in PDB:3CGI by side chains.
CC {ECO:0000269|PubMed:18786396}.
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}.
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 EutS/PduU family. {ECO:0000255|PROSITE-
CC ProRule:PRU01279, ECO:0000305}.
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DR EMBL; AF026270; AAD39019.1; -; Genomic_DNA.
DR EMBL; AE006468; AAL20959.1; -; Genomic_DNA.
DR RefSeq; NP_461000.1; NC_003197.2.
DR RefSeq; WP_000441103.1; NC_003197.2.
DR PDB; 3CGI; X-ray; 1.80 A; A/B/C/D=1-116.
DR PDBsum; 3CGI; -.
DR AlphaFoldDB; P0A1D1; -.
DR SMR; P0A1D1; -.
DR STRING; 99287.STM2055; -.
DR PaxDb; P0A1D1; -.
DR EnsemblBacteria; AAL20959; AAL20959; STM2055.
DR GeneID; 1253576; -.
DR GeneID; 64335876; -.
DR GeneID; 66587171; -.
DR KEGG; stm:STM2055; -.
DR PATRIC; fig|99287.12.peg.2177; -.
DR HOGENOM; CLU_143326_0_0_6; -.
DR OMA; HIIPNPQ; -.
DR PhylomeDB; P0A1D1; -.
DR BioCyc; SENT99287:STM2055-MON; -.
DR UniPathway; UPA00621; -.
DR EvolutionaryTrace; P0A1D1; -.
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 CDD; cd07046; BMC_PduU-EutS; 1.
DR Gene3D; 3.30.70.1710; -; 1.
DR InterPro; IPR044870; BMC_CP.
DR InterPro; IPR000249; BMC_dom.
DR InterPro; IPR037233; CcmK-like_sf.
DR InterPro; IPR009307; EutS/PduU/CutR.
DR PANTHER; PTHR40449; PTHR40449; 1.
DR Pfam; PF00936; BMC; 1.
DR PIRSF; PIRSF012296; EutS_PduU; 1.
DR SMART; SM00877; BMC; 1.
DR SUPFAM; SSF143414; SSF143414; 1.
DR PROSITE; PS51931; BMC_CP; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Bacterial microcompartment; Reference proteome; Transport.
FT CHAIN 1..116
FT /note="Bacterial microcompartment shell protein PduU"
FT /id="PRO_0000201526"
FT DOMAIN 9..108
FT /note="BMC circularly permuted"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01279"
FT STRAND 9..14
FT /evidence="ECO:0007829|PDB:3CGI"
FT STRAND 19..28
FT /evidence="ECO:0007829|PDB:3CGI"
FT HELIX 31..36
FT /evidence="ECO:0007829|PDB:3CGI"
FT STRAND 45..53
FT /evidence="ECO:0007829|PDB:3CGI"
FT HELIX 56..66
FT /evidence="ECO:0007829|PDB:3CGI"
FT STRAND 67..76
FT /evidence="ECO:0007829|PDB:3CGI"
FT TURN 77..80
FT /evidence="ECO:0007829|PDB:3CGI"
FT STRAND 81..86
FT /evidence="ECO:0007829|PDB:3CGI"
FT HELIX 88..106
FT /evidence="ECO:0007829|PDB:3CGI"
FT STRAND 114..116
FT /evidence="ECO:0007829|PDB:3CGI"
SQ SEQUENCE 116 AA; 12476 MW; 39BEFE5E38F0D1F6 CRC64;
MERQPTTDRM IQEYVPGKQV TLAHLIANPG KDLFKKLGLQ DAVSAIGILT ITPSEASIIA
CDIATKSGAV EIGFLDRFTG AVVLTGDVSA VEYALKQVTR TLGEMMQFTT CSITRT
