PDUD_SALTY
ID PDUD_SALTY Reviewed; 224 AA.
AC O31041; Q7BV84;
DT 09-FEB-2010, integrated into UniProtKB/Swiss-Prot.
DT 01-JAN-1998, sequence version 1.
DT 03-AUG-2022, entry version 101.
DE RecName: Full=Propanediol dehydratase medium subunit;
DE EC=4.2.1.28 {ECO:0000269|PubMed:21821773};
DE AltName: Full=Diol dehydratase medium subunit;
DE Short=DDH medium subunit;
DE AltName: Full=Propanediol utilization protein PduD;
GN Name=pduD {ECO:0000303|PubMed:9352910}; OrderedLocusNames=STM2041;
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], FUNCTION, CATALYTIC ACTIVITY, AND
RP SUBUNIT.
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 [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], PATHWAY, SUBCELLULAR LOCATION, AND
RP 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 [3]
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 [4]
RP COFACTOR.
RX PubMed=2166132; DOI=10.1099/00221287-136-5-887;
RA Jeter R.M.;
RT "Cobalamin-dependent 1,2-propanediol utilization by Salmonella
RT typhimurium.";
RL J. Gen. Microbiol. 136:887-896(1990).
RN [5]
RP INDUCTION.
RX PubMed=1312999; DOI=10.1128/jb.174.7.2253-2266.1992;
RA Bobik T.A., Ailion M., Roth J.R.;
RT "A single regulatory gene integrates control of vitamin B12 synthesis and
RT propanediol degradation.";
RL J. Bacteriol. 174:2253-2266(1992).
RN [6]
RP DISRUPTION PHENOTYPE, AND FUNCTION IN PROPANEDIOL UTILIZATION.
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 [7]
RP SUBCELLULAR LOCATION.
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 [8]
RP IDENTIFICATION BY MASS SPECTROMETRY, 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 [9]
RP 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 [10]
RP FUNCTION, SUBCELLULAR LOCATION, DOMAIN, AND MUTAGENESIS OF 2-GLU--THR-35.
RC STRAIN=LT2;
RX PubMed=21821773; DOI=10.1128/jb.05661-11;
RA Fan C., Bobik T.A.;
RT "The N-terminal region of the medium subunit (PduD) packages
RT adenosylcobalamin-dependent diol dehydratase (PduCDE) into the Pdu
RT microcompartment.";
RL J. Bacteriol. 193:5623-5628(2011).
RN [11]
RP ACTIVITY REGULATION.
RC STRAIN=LT2;
RX PubMed=25713376; DOI=10.1073/pnas.1423672112;
RA Chowdhury C., Chun S., Pang A., Sawaya M.R., Sinha S., Yeates T.O.,
RA Bobik T.A.;
RT "Selective molecular transport through the protein shell of a bacterial
RT microcompartment organelle.";
RL Proc. Natl. Acad. Sci. U.S.A. 112:2990-2995(2015).
RN [12]
RP FUNCTION, SUBCELLULAR LOCATION, AND DOMAIN.
RC STRAIN=LT2;
RX PubMed=26283792; DOI=10.1074/jbc.m115.651919;
RA Jakobson C.M., Kim E.Y., Slininger M.F., Chien A., Tullman-Ercek D.;
RT "Localization of proteins to the 1,2-propanediol utilization
RT microcompartment by non-native signal sequences is mediated by a common
RT hydrophobic motif.";
RL J. Biol. Chem. 290:24519-24533(2015).
RN [13]
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: Part of the PduCDE complex that catalyzes the dehydration of
CC 1,2-propanediol (1,2-PD) to propionaldehyde. Required for S.typhimurium
CC growth on 1,2-PD as the sole carbon and energy source (Probable)
CC (PubMed:9023178). This subunit is directly targeted to the bacterial
CC microcompartment (BMC) dedicated to 1,2-PD degradation, and is also
CC responsible for targeting the other 2 subunits (pduC and pduE)
CC (PubMed:21821773, PubMed:26283792). {ECO:0000269|PubMed:21821773,
CC ECO:0000269|PubMed:26283792, ECO:0000269|PubMed:9023178,
CC ECO:0000305|PubMed:9352910}.
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:25713376, ECO:0000305|PubMed:28475631}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=propane-1,2-diol = H2O + propanal; Xref=Rhea:RHEA:14569,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:16997, ChEBI:CHEBI:17153; EC=4.2.1.28;
CC Evidence={ECO:0000269|PubMed:9352910};
CC -!- COFACTOR:
CC Name=adenosylcob(III)alamin; Xref=ChEBI:CHEBI:18408;
CC Evidence={ECO:0000269|PubMed:2166132};
CC -!- ACTIVITY REGULATION: Inhibited by glycerol.
CC {ECO:0000269|PubMed:25713376}.
CC -!- PATHWAY: Polyol metabolism; 1,2-propanediol degradation.
CC {ECO:0000305|PubMed:10498708}.
CC -!- SUBUNIT: The propanediol dehydratase enzyme is a heterotrimeric complex
CC composed of a large (PduC), a medium (PduD) and a small (PduE) subunit.
CC {ECO:0000269|PubMed:9352910}.
CC -!- SUBCELLULAR LOCATION: Bacterial microcompartment
CC {ECO:0000269|PubMed:10498708, ECO:0000269|PubMed:11844753,
CC ECO:0000269|PubMed:12923081, ECO:0000269|PubMed:21821773,
CC ECO:0000269|PubMed:26283792}. Note=Probably located inside the BMC
CC shell. {ECO:0000305|PubMed:10498708, ECO:0000305|PubMed:21821773}.
CC -!- INDUCTION: BMC production is induced by growth on 1,2-PD vitamin B12
CC medium (PubMed:10498708). By either propanediol or glycerol.
CC {ECO:0000269|PubMed:10498708, ECO:0000269|PubMed:1312999}.
CC -!- DOMAIN: The first 18 residues targets this enzyme and foreign proteins
CC (tested with GST and eGFP) to the BMC. The cargo is only detected by
CC Western blot in broken shells, strongly suggesting this protein is
CC normally found inside the BMC and not on its exterior (PubMed:21821773,
CC PubMed:26283792). PduD and PduP compete for encapsulation in BMCs,
CC suggesting PduD also binds to PduA and/or PduJ (PubMed:26283792).
CC {ECO:0000269|PubMed:21821773, ECO:0000269|PubMed:26283792}.
CC -!- DISRUPTION PHENOTYPE: Cells lacking this gene are defective in aerobic
CC degradation of propanediol and display no propanediol dehydratase
CC activity. A triple pduC-pduD-pduE deletion releases no acetaldehyde
CC when grown on propanediol (PubMed:16585748).
CC {ECO:0000269|PubMed:16585748, ECO:0000269|PubMed:9023178}.
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 diol/glycerol dehydratase medium subunit
CC family. {ECO:0000305}.
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DR EMBL; AF026270; AAB84103.1; -; Genomic_DNA.
DR EMBL; AE006468; AAL20945.1; -; Genomic_DNA.
DR RefSeq; NP_460986.1; NC_003197.2.
DR RefSeq; WP_000405048.1; NC_003197.2.
DR AlphaFoldDB; O31041; -.
DR SMR; O31041; -.
DR STRING; 99287.STM2041; -.
DR PaxDb; O31041; -.
DR EnsemblBacteria; AAL20945; AAL20945; STM2041.
DR GeneID; 1253562; -.
DR KEGG; stm:STM2041; -.
DR PATRIC; fig|99287.12.peg.2163; -.
DR HOGENOM; CLU_104657_0_0_6; -.
DR OMA; VIHQRGL; -.
DR PhylomeDB; O31041; -.
DR BioCyc; MetaCyc:STM2041-MON; -.
DR BioCyc; SENT99287:STM2041-MON; -.
DR UniPathway; UPA00621; -.
DR Proteomes; UP000001014; Chromosome.
DR GO; GO:0031472; C:propanediol degradation polyhedral organelle; IDA:UniProtKB.
DR GO; GO:0031419; F:cobalamin binding; IEA:UniProtKB-KW.
DR GO; GO:0050215; F:propanediol dehydratase activity; IEA:UniProtKB-EC.
DR GO; GO:0051144; P:propanediol catabolic process; IEA:UniProtKB-UniPathway.
DR Gene3D; 3.40.50.10150; -; 1.
DR InterPro; IPR010254; B12-dep_deHydtase_bsu.
DR InterPro; IPR003208; Dehydtase/Dehydtase_re.
DR InterPro; IPR025541; Ppandiol/glycerol_DHydtase_msu.
DR Pfam; PF02288; Dehydratase_MU; 1.
DR PIRSF; PIRSF018506; Prpndl_dhdrts_md; 1.
DR SUPFAM; SSF52968; SSF52968; 1.
PE 1: Evidence at protein level;
KW Bacterial microcompartment; Cobalamin; Cobalt; Lyase; Reference proteome.
FT CHAIN 1..224
FT /note="Propanediol dehydratase medium subunit"
FT /id="PRO_0000391459"
FT REGION 1..18
FT /note="Targets protein to the BMC"
FT /evidence="ECO:0000269|PubMed:21821773"
FT MUTAGEN 2..35
FT /note="Missing: Enzyme no longer associated with BMCs, no
FT effect on enzyme activity."
FT /evidence="ECO:0000269|PubMed:21821773"
SQ SEQUENCE 224 AA; 24173 MW; 370B145E9AD7A5BE CRC64;
MEINEKLLRQ IIEDVLRDMK GSDKPVSFNA PAASTAPQTA APAGDGFLTE VGEARQGTQQ
DEVIIAVGPA FGLAQTVNIV GLPHKSILRE VIAGIEEEGI KARVIRCFKS SDVAFVAVEG
NRLSGSGISI GIQSKGTTVI HQQGLPPLSN LELFPQAPLL TLETYRQIGK NAARYAKRES
PQPVPTLNDQ MARPKYQAKS AILHIKETKY VVTGKNPQEL RVAL
