PDUS_SALTY
ID PDUS_SALTY Reviewed; 451 AA.
AC Q9XDM9; Q7BV74;
DT 25-MAY-2022, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1999, sequence version 1.
DT 03-AUG-2022, entry version 142.
DE RecName: Full=Cobalamin reductase PduS {ECO:0000303|PubMed:20656910};
DE AltName: Full=Propanediol utilization protein PduS;
GN Name=pduS {ECO:0000303|PubMed:10498708}; OrderedLocusNames=STM2053;
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 PROTEIN SEQUENCE OF 59-72; 98-113; 241-249; 276-291 AND 395-412, FUNCTION,
RP FMN COFACTOR, FE-S COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT,
RP INTERACTION WITH PDUO, SUBCELLULAR LOCATION, AND DISRUPTION PHENOTYPE.
RC STRAIN=LT2;
RX PubMed=20656910; DOI=10.1128/jb.00575-10;
RA Cheng S., Bobik T.A.;
RT "Characterization of the PduS cobalamin reductase of Salmonella enterica
RT and its role in the Pdu microcompartment.";
RL J. Bacteriol. 192:5071-5080(2010).
RN [4]
RP BACTERIAL MICROCOMPARTMENT ABUNDANCE.
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 [5]
RP FUNCTION, FE-S COFACTOR, AND SUBUNIT.
RC STRAIN=LT2;
RX PubMed=15817784; DOI=10.1099/mic.0.27755-0;
RA Sampson E.M., Johnson C.L.V., Bobik T.A.;
RT "Biochemical evidence that the pduS gene encodes a bifunctional cobalamin
RT reductase.";
RL Microbiology 151:1169-1177(2005).
RN [6]
RP POSSIBLE REACTION MECHANISM, AND POSSIBLE FLAVIN COFACTOR.
RC STRAIN=TR6583;
RX PubMed=19933577; DOI=10.1074/jbc.m109.059485;
RA Mera P.E., Escalante-Semerena J.C.;
RT "Dihydroflavin-driven adenosylation of 4-coordinate Co(II) corrinoids: are
RT cobalamin reductases enzymes or electron transfer proteins?";
RL J. Biol. Chem. 285:2911-2917(2010).
RN [7]
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 protein that aids in conversion of cob(III)alamin to
CC cob(II)alamin and then to cob(I)alamin in the bacterial
CC microcompartment (BMC) dedicated to 1,2-propanediol (1,2-PD)
CC degradation (PubMed:15817784, PubMed:20656910). The latter step
CC requires PduO. No free cob(I)alamin is released, suggesting a complex
CC is formed with PduO that finishes conversion to adenosylcobalamin. PduS
CC and PduO allow regeneration of the adenosylcobalamin cofactor within
CC the BMC (PubMed:15817784). Another study showed reduction of
CC cob(II)alamin to cob(I)alamin in the absence of PduO. Both reactions
CC require NADH. Cyanocobalamin (CN-Cbl) is not a substrate for the first
CC reaction (PubMed:20656910). Cobalamin reduction probably occurs
CC spontaneously in the presence of free reduced flavin nucleotides, this
CC protein may be involved in electron transfer for this reduction
CC (Probable). {ECO:0000269|PubMed:15817784, ECO:0000269|PubMed:20656910,
CC ECO:0000305|PubMed:19933577}.
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:0000255|PROSITE-ProRule:PRU00711,
CC ECO:0000305|PubMed:15817784, ECO:0000305|PubMed:20656910};
CC Note=Binds 2 [4Fe-4S] clusters (By similarity). The two centers are
CC coupled but must possess different redox potentials (By similarity).
CC {ECO:0000250|UniProtKB:B1VB77, ECO:0000255|PROSITE-ProRule:PRU00711};
CC -!- COFACTOR:
CC Name=FMN; Xref=ChEBI:CHEBI:58210;
CC Evidence={ECO:0000269|PubMed:20656910};
CC Note=Binds one FMN non-covalently per monomer.
CC {ECO:0000269|PubMed:20656910};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=10.1 uM for NADH in cob(III)alamin reductase
CC {ECO:0000269|PubMed:20656910};
CC KM=67.5 uM for hydroxycobalamin in cob(III)alamin reductase
CC {ECO:0000269|PubMed:20656910};
CC KM=27.5 uM for NADH in cob(II)alamin reductase
CC {ECO:0000269|PubMed:20656910};
CC KM=72.4 uM for cob(II)alamin in cob(II)alamin reductase
CC {ECO:0000269|PubMed:20656910};
CC Vmax=43.1 mmol/min/mg enzyme for NADH in cob(III)alamin reductase
CC {ECO:0000269|PubMed:20656910};
CC Vmax=46.6 mmol/min/mg enzyme for hydroxycobalamin in cob(III)alamin
CC reductase {ECO:0000269|PubMed:20656910};
CC Vmax=56.8 nmol/min/mg enzyme for NADH in cob(II)alamin reductase
CC {ECO:0000269|PubMed:20656910};
CC Vmax=64.7 nmol/min/mg enzyme for cob(II)alamin in cob(II)alamin
CC reductase {ECO:0000269|PubMed:20656910};
CC pH dependence:
CC Optimum pH for cob(III)alamin reductase activity is pH 9.5, no major
CC effect of pH was seen on cob(II)alamin reductase activity between pH
CC 7-10. {ECO:0000269|PubMed:20656910};
CC Temperature dependence:
CC Optimum temperature is 37 degrees Celsius for cob(III)alamin
CC reductase and 42 degrees Celsius for cob(II)alamin reductase.
CC {ECO:0000269|PubMed:20656910};
CC -!- PATHWAY: Polyol metabolism; 1,2-propanediol degradation.
CC {ECO:0000305|PubMed:10498708}.
CC -!- SUBUNIT: Monomeric when purified anaerobically, dimeric under aerobic
CC conditions (PubMed:20656910). Forms a complex with PduO
CC (PubMed:15817784, PubMed:20656910). Interacts with PduT, probably via
CC the N-terminus of PduS (By similarity). {ECO:0000250|UniProtKB:B1VB77,
CC ECO:0000269|PubMed:15817784, ECO:0000269|PubMed:20656910}.
CC -!- SUBCELLULAR LOCATION: Bacterial microcompartment
CC {ECO:0000269|PubMed:20656910}.
CC -!- INDUCTION: BMC production is induced by growth on 1,2-PD vitamin B12
CC medium. {ECO:0000269|PubMed:10498708}.
CC -!- DISRUPTION PHENOTYPE: Grows more slowly and to a lower cell density
CC than wild-type. {ECO:0000269|PubMed:20656910}.
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 PduS cobalamin reductase family.
CC {ECO:0000305}.
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DR EMBL; AF026270; AAD39017.1; -; Genomic_DNA.
DR EMBL; AE006468; AAL20957.1; -; Genomic_DNA.
DR RefSeq; NP_460998.1; NC_003197.2.
DR RefSeq; WP_000100782.1; NC_003197.2.
DR AlphaFoldDB; Q9XDM9; -.
DR IntAct; Q9XDM9; 1.
DR STRING; 99287.STM2053; -.
DR PaxDb; Q9XDM9; -.
DR EnsemblBacteria; AAL20957; AAL20957; STM2053.
DR GeneID; 1253574; -.
DR KEGG; stm:STM2053; -.
DR PATRIC; fig|99287.12.peg.2175; -.
DR HOGENOM; CLU_010808_0_0_6; -.
DR OMA; CEQCRMC; -.
DR PhylomeDB; Q9XDM9; -.
DR BioCyc; MetaCyc:STM2053-MON; -.
DR BioCyc; SENT99287:STM2053-MON; -.
DR UniPathway; UPA00621; -.
DR Proteomes; UP000001014; Chromosome.
DR GO; GO:0016020; C:membrane; IEA:InterPro.
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:0009055; F:electron transfer activity; IEA:InterPro.
DR GO; GO:0010181; F:FMN binding; IDA:UniProtKB.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0009236; P:cobalamin biosynthetic process; IEA:UniProtKB-KW.
DR GO; GO:0051144; P:propanediol catabolic process; IEA:UniProtKB-UniPathway.
DR Gene3D; 1.10.1060.10; -; 1.
DR Gene3D; 3.40.50.11540; -; 1.
DR InterPro; IPR017896; 4Fe4S_Fe-S-bd.
DR InterPro; IPR009051; Helical_ferredxn.
DR InterPro; IPR010208; Ion_transpt_RnfC/RsxC.
DR InterPro; IPR011538; Nuo51_FMN-bd.
DR InterPro; IPR037225; Nuo51_FMN-bd_sf.
DR InterPro; IPR017054; PduS.
DR InterPro; IPR026902; RnfC_N.
DR InterPro; IPR019554; Soluble_ligand-bd.
DR PANTHER; PTHR43034; PTHR43034; 2.
DR Pfam; PF01512; Complex1_51K; 1.
DR Pfam; PF13375; RnfC_N; 1.
DR Pfam; PF10531; SLBB; 1.
DR PIRSF; PIRSF036408; PduS_prd; 1.
DR SUPFAM; SSF142019; SSF142019; 1.
DR PROSITE; PS00198; 4FE4S_FER_1; 1.
DR PROSITE; PS51379; 4FE4S_FER_2; 2.
PE 1: Evidence at protein level;
KW 4Fe-4S; Bacterial microcompartment; Cobalamin biosynthesis;
KW Direct protein sequencing; Electron transport; Flavoprotein; FMN; Iron;
KW Iron-sulfur; Metal-binding; NAD; Reference proteome; Repeat; Transport.
FT CHAIN 1..451
FT /note="Cobalamin reductase PduS"
FT /id="PRO_0000454284"
FT DOMAIN 255..284
FT /note="4Fe-4S ferredoxin-type 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00711"
FT DOMAIN 300..330
FT /note="4Fe-4S ferredoxin-type 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00711"
FT BINDING 264
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00711"
FT BINDING 267
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00711"
FT BINDING 270
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00711"
FT BINDING 274
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00711"
FT BINDING 309
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00711"
FT BINDING 312
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00711"
FT BINDING 315
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00711"
FT BINDING 320
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00711"
SQ SEQUENCE 451 AA; 48389 MW; 9B7710F12985A0E0 CRC64;
MSTAINSVEM SLSADEIRER VRAAGVVGAG GAGFPAHVKL QAQVEIFLVN AAECEPMLKV
DQQLMWQQAA RLVRGVQYAM TATGAREGVI ALKEKYRRAI DALTPLLPDG IRLHILPDVY
PAGDEVLTIW MATGRRVAPA ALPASVGVVV NNVQTVLNIA RAVEQRFPVT RRTLTVNGAV
ARPLTVTVPI GMSLREVLAL AGGATVDDPG FINGGPMMGG LITSLDNPVT KTTGGLLVLP
KSHPLIQRRM QDERTVLSVA RTVCEQCRLC TDLCPRHLIG HELSPHLLVR AVNFHQAATP
QLLLSALTCS ECNVCESVAC PVGISPMRIN RMLKRELRAQ NQRYEGPLNP ADEMAKYRLV
PVKRLIAKLG LSPWYQEAPL VEEEPSVEKV TLQLRQHIGA SAVANVAVGE RVTRGQCVAD
VPPGALGAPI HASIDGVVSA ISEQAITVVR G
