PDUO_SALTY
ID PDUO_SALTY Reviewed; 336 AA.
AC Q8ZNR5; A0A1A9TAI7; Q9XDN2;
DT 23-FEB-2022, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2002, sequence version 1.
DT 03-AUG-2022, entry version 98.
DE RecName: Full=Corrinoid adenosyltransferase PduO {ECO:0000303|PubMed:11160088};
DE EC=2.5.1.- {ECO:0000269|PubMed:11160088, ECO:0000269|PubMed:15547259};
DE AltName: Full=ATP:co(I)rrinoid adenosyltransferase PduO;
DE Short=ACA {ECO:0000303|PubMed:27446048};
DE AltName: Full=Propanediol utilization protein PduO;
GN Name=pduO {ECO:0000303|PubMed:10498708}; OrderedLocusNames=STM2050;
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, 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, CATALYTIC ACTIVITY, DISRUPTION PHENOTYPE, AND SEQUENCE REVISION.
RC STRAIN=LT2;
RX PubMed=11160088; DOI=10.1128/jb.183.5.1577-1584.2001;
RA Johnson C.L., Pechonick E., Park S.D., Havemann G.D., Leal N.A.,
RA Bobik T.A.;
RT "Functional genomic, biochemical, and genetic characterization of the
RT Salmonella pduO gene, an ATP:cob(I)alamin adenosyltransferase gene.";
RL J. Bacteriol. 183:1577-1584(2001).
RN [5]
RP FUNCTION, CATALYTIC ACTIVITY, COFACTOR, ACTIVITY REGULATION,
RP BIOPHYSICOCHEMICAL PROPERTIES, AND DOMAIN.
RX PubMed=15547259; DOI=10.1128/jb.186.23.7881-7887.2004;
RA Johnson C.L., Buszko M.L., Bobik T.A.;
RT "Purification and initial characterization of the Salmonella enterica PduO
RT ATP:Cob(I)alamin adenosyltransferase.";
RL J. Bacteriol. 186:7881-7887(2004).
RN [6]
RP FUNCTION, SUBUNIT, AND INTERACTION WITH PDUS.
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 [7]
RP FUNCTION, CATALYTIC ACTIVITY, FMN COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES,
RP SUBUNIT, INTERACTION WITH PDUS, 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 [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:0000312|PDB:5CX7, ECO:0007744|PDB:5CX7}
RP X-RAY CRYSTALLOGRAPHY (1.97 ANGSTROMS) OF 194-336 IN COMPLEX WITH HEME AND
RP MAGNESIUM, FUNCTION, HEME B COFACTOR, SUBUNIT, DOMAIN, DISRUPTION
RP PHENOTYPE, AND MUTAGENESIS OF HIS-207.
RC STRAIN=ATCC 14028 / SGSC 2980 / CDC 6516-60 / NCTC 12023
RC {ECO:0000303|PubMed:27446048};
RX PubMed=27446048; DOI=10.3389/fmicb.2016.01010;
RA Ortiz de Orue Lucana D., Hickey N., Hensel M., Klare J.P., Geremia S.,
RA Tiufiakova T., Torda A.E.;
RT "The Crystal Structure of the C-Terminal Domain of the Salmonella enterica
RT PduO Protein: An Old Fold with a New Heme-Binding Mode.";
RL Front. Microbiol. 7:1010-1010(2016).
CC -!- FUNCTION: Converts cob(I)alamin to adenosylcobalamin
CC (adenosylcob(III)alamin), the cofactor for propanediol dehydratase.
CC Found in the bacterial microcompartment (BMC) dedicated to 1,2-
CC propanediol (1,2-PD) degradation (PubMed:11160088, PubMed:15547259,
CC PubMed:27446048, PubMed:15817784, PubMed:20656910). For
CC adenosylcobalamin synthesis dATP can replace ATP, but no other
CC nucleotides will substitute (PubMed:15547259). PduS and PduO allow
CC regeneration of the adenosylcobalamin cofactor within the BMC
CC (Probable). {ECO:0000269|PubMed:11160088, ECO:0000269|PubMed:15547259,
CC ECO:0000269|PubMed:15817784, ECO:0000269|PubMed:20656910,
CC ECO:0000269|PubMed:27446048, 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 -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + cob(I)alamin-[corrinoid adenosyltransferase] =
CC adenosylcob(III)alamin + apo-[corrinoid adenosyltransferase] +
CC triphosphate; Xref=Rhea:RHEA:56796, Rhea:RHEA-COMP:14743, Rhea:RHEA-
CC COMP:14744, ChEBI:CHEBI:18036, ChEBI:CHEBI:18408, ChEBI:CHEBI:30616,
CC ChEBI:CHEBI:60488, ChEBI:CHEBI:83228;
CC Evidence={ECO:0000269|PubMed:15547259, ECO:0000269|PubMed:27446048,
CC ECO:0000305|PubMed:11160088};
CC -!- COFACTOR:
CC Name=heme b; Xref=ChEBI:CHEBI:60344;
CC Evidence={ECO:0000269|PubMed:27446048, ECO:0007744|PDB:5CX7};
CC Note=Stoichiometry of heme binding is 2 PduOC:1 heme; the binding
CC pocket is formed by a PduOC dimer. Full-length PduO also binds heme.
CC {ECO:0000269|PubMed:27446048};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:15547259, ECO:0000269|PubMed:27446048};
CC Note=Mn(2+) and Co(2+) are almost as active as Mg(2+) for
CC adenosylcobalamin synthesis. {ECO:0000269|PubMed:15547259};
CC -!- ACTIVITY REGULATION: Inhibited by ADP but not significantly by other
CC nucleotides, inhibited by diphosphate and less well by triphosphate.
CC {ECO:0000269|PubMed:15547259}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=19.8 uM for ATP {ECO:0000269|PubMed:15547259};
CC KM=4.5 uM for cob(I)alamin {ECO:0000269|PubMed:15547259};
CC Vmax=243 nmol/min/mg enzyme {ECO:0000269|PubMed:15547259};
CC -!- PATHWAY: Polyol metabolism; 1,2-propanediol degradation.
CC {ECO:0000269|PubMed:10498708}.
CC -!- PATHWAY: Cofactor biosynthesis; adenosylcobalamin biosynthesis.
CC {ECO:0000305|PubMed:10498708}.
CC -!- SUBUNIT: The C-terminal domain (PduOC) forms stable octomers and also
CC crystallizes as an octomer (PubMed:27446048). Forms a complex with PduS
CC (PubMed:15817784, PubMed:20656910). {ECO:0000269|PubMed:15817784,
CC ECO:0000269|PubMed:20656910, ECO:0000269|PubMed:27446048}.
CC -!- SUBCELLULAR LOCATION: Bacterial microcompartment
CC {ECO:0000305|PubMed:12923081}.
CC -!- INDUCTION: BMC production is induced by growth on 1,2-PD vitamin B12
CC medium. {ECO:0000269|PubMed:10498708}.
CC -!- DOMAIN: The N-terminus (PduON, residues 1-185) has adenosyltransferase
CC activity in vivo and in vitro; it partially complements a deletion
CC mutant for growth on 1,2-PD (PubMed:15547259, PubMed:27446048). The C-
CC terminal domain (PduOC, residues 194-336) is required for full
CC complemention of a pduO deletion (PubMed:27446048).
CC {ECO:0000269|PubMed:15547259, ECO:0000269|PubMed:27446048}.
CC -!- DISRUPTION PHENOTYPE: Decreased growth on 1,2-PD cyanocobalamin medium;
CC no growth is seen in a double cobA-pduO deletion.
CC {ECO:0000269|PubMed:11160088, ECO:0000269|PubMed:27446048}.
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 Cob(I)alamin adenosyltransferase family.
CC PduO subfamily. {ECO:0000305}.
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DR EMBL; AF026270; AAD39014.1; -; Genomic_DNA.
DR EMBL; AE006468; AAL20954.1; -; Genomic_DNA.
DR RefSeq; NP_460995.1; NC_003197.2.
DR RefSeq; WP_001029484.1; NC_003197.2.
DR PDB; 5CX7; X-ray; 1.97 A; A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P=194-336.
DR PDBsum; 5CX7; -.
DR AlphaFoldDB; Q8ZNR5; -.
DR SMR; Q8ZNR5; -.
DR IntAct; Q8ZNR5; 1.
DR STRING; 99287.STM2050; -.
DR PaxDb; Q8ZNR5; -.
DR EnsemblBacteria; AAL20954; AAL20954; STM2050.
DR GeneID; 1253571; -.
DR KEGG; stm:STM2050; -.
DR PATRIC; fig|99287.12.peg.2172; -.
DR HOGENOM; CLU_068893_0_0_6; -.
DR OMA; IFWFSAE; -.
DR PhylomeDB; Q8ZNR5; -.
DR BioCyc; MetaCyc:STM2050-MON; -.
DR BioCyc; SENT99287:STM2050-MON; -.
DR UniPathway; UPA00148; -.
DR UniPathway; UPA00621; -.
DR Proteomes; UP000001014; Chromosome.
DR GO; GO:0031472; C:propanediol degradation polyhedral organelle; IDA:UniProtKB.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0008817; F:cob(I)yrinic acid a,c-diamide adenosyltransferase activity; IBA:GO_Central.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0009236; P:cobalamin biosynthetic process; IEA:UniProtKB-UniPathway.
DR GO; GO:0051144; P:propanediol catabolic process; IEA:UniProtKB-UniPathway.
DR Gene3D; 1.20.1200.10; -; 1.
DR Gene3D; 3.30.450.150; -; 1.
DR InterPro; IPR016030; CblAdoTrfase-like.
DR InterPro; IPR036451; CblAdoTrfase-like_sf.
DR InterPro; IPR009221; PduO.
DR InterPro; IPR029499; PduO-typ.
DR InterPro; IPR005624; PduO/GlcC-like.
DR InterPro; IPR038084; PduO/GlcC-like_sf.
DR PANTHER; PTHR12213; PTHR12213; 1.
DR Pfam; PF01923; Cob_adeno_trans; 1.
DR Pfam; PF03928; Haem_degrading; 1.
DR PIRSF; PIRSF036411; ATR_PduO; 1.
DR SUPFAM; SSF143744; SSF143744; 1.
DR SUPFAM; SSF89028; SSF89028; 1.
DR TIGRFAMs; TIGR00636; PduO_Nterm; 1.
PE 1: Evidence at protein level;
KW 3D-structure; ATP-binding; Bacterial microcompartment;
KW Cobalamin biosynthesis; Heme; Iron; Magnesium; Metal-binding;
KW Nucleotide-binding; Reference proteome; Transferase.
FT CHAIN 1..336
FT /note="Corrinoid adenosyltransferase PduO"
FT /id="PRO_0000454282"
FT REGION 1..185
FT /note="PduON"
FT /evidence="ECO:0000305|PubMed:15547259,
FT ECO:0000305|PubMed:27446048"
FT REGION 194..336
FT /note="PduOC"
FT /evidence="ECO:0000305|PubMed:27446048"
FT BINDING 207
FT /ligand="heme"
FT /ligand_id="ChEBI:CHEBI:30413"
FT /ligand_part="Fe"
FT /ligand_part_id="ChEBI:CHEBI:18248"
FT /note="axial binding residue"
FT /evidence="ECO:0007744|PDB:5CX7"
FT BINDING 215
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0007744|PDB:5CX7"
FT BINDING 218
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0007744|PDB:5CX7"
FT MUTAGEN 207
FT /note="H->A: PduOC is no longer red, the mutation in the
FT whole protein does not complement as well as wild-type."
FT /evidence="ECO:0000269|PubMed:27446048"
FT CONFLICT 94..114
FT /note="EAAIDRAMARVEPLHSFILPG -> GSRYRSGDGPRRTAAQLYFTR (in
FT Ref. 1; AAD39014)"
FT /evidence="ECO:0000305"
FT CONFLICT 294
FT /note="G -> GG (in Ref. 1; AAD39014)"
FT /evidence="ECO:0000305"
FT HELIX 203..219
FT /evidence="ECO:0007829|PDB:5CX7"
FT STRAND 225..230
FT /evidence="ECO:0007829|PDB:5CX7"
FT STRAND 235..240
FT /evidence="ECO:0007829|PDB:5CX7"
FT HELIX 248..261
FT /evidence="ECO:0007829|PDB:5CX7"
FT HELIX 266..269
FT /evidence="ECO:0007829|PDB:5CX7"
FT TURN 270..273
FT /evidence="ECO:0007829|PDB:5CX7"
FT TURN 278..281
FT /evidence="ECO:0007829|PDB:5CX7"
FT HELIX 282..285
FT /evidence="ECO:0007829|PDB:5CX7"
FT TURN 286..288
FT /evidence="ECO:0007829|PDB:5CX7"
FT STRAND 293..301
FT /evidence="ECO:0007829|PDB:5CX7"
FT STRAND 304..314
FT /evidence="ECO:0007829|PDB:5CX7"
FT HELIX 316..328
FT /evidence="ECO:0007829|PDB:5CX7"
SQ SEQUENCE 336 AA; 36634 MW; E33379D4DA61171F CRC64;
MAIYTRTGDA GTTSLFTGQR VSKTHPRVEA YGTLDELNAA LSLCACAAAD ENHRTLLEAI
QQQLFWFSAE LASDSEQPSP KQRYISSEEI SALEAAIDRA MARVEPLHSF ILPGRCEAAS
RLHFARTLAR RAERRLVELA TEVNVRQVLM RYINRLSDCL YALARAEDSD AHQANIIREV
SKRYLAACQP PHSKETTPVA LSFHDLHQLT RAAVERAQQL QVPVVVSIVD AHGTETVTWR
MPDALLVSSE LAPKKAWTAV AMKTATHELS DVVQPGAALY GLESHLQGKV VTFGGGYALW
RDGILIGGLG ISGGSVEQDM DIAQTAIAAI NVGTHQ
