PDUX_SALTY
ID PDUX_SALTY Reviewed; 300 AA.
AC Q9XDM4; H9L4E0; Q7BV72;
DT 06-MAR-2013, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1999, sequence version 1.
DT 03-AUG-2022, entry version 107.
DE RecName: Full=L-threonine kinase {ECO:0000303|PubMed:18308727};
DE EC=2.7.1.177 {ECO:0000269|PubMed:18308727};
DE AltName: Full=Propanediol utilization protein PduX;
GN Name=pduX {ECO:0000303|PubMed:10498708}; OrderedLocusNames=STM2058;
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 / SGSC1412 / ATCC 700720;
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 DISRUPTION PHENOTYPE.
RC STRAIN=LT2;
RX PubMed=12700259; DOI=10.1128/jb.185.9.2802-2810.2003;
RA Palacios S., Starai V.J., Escalante-Semerena J.C.;
RT "Propionyl coenzyme A is a common intermediate in the 1,2-propanediol and
RT propionate catabolic pathways needed for expression of the prpBCDE operon
RT during growth of Salmonella enterica on 1,2-propanediol.";
RL J. Bacteriol. 185:2802-2810(2003).
RN [4]
RP FUNCTION, CATALYTIC ACTIVITY, PATHWAY, BIOPHYSICOCHEMICAL PROPERTIES, AND
RP DISRUPTION PHENOTYPE.
RC STRAIN=LT2 / SGSC1412 / ATCC 700720;
RX PubMed=18308727; DOI=10.1074/jbc.m800287200;
RA Fan C., Bobik T.A.;
RT "The PduX enzyme of Salmonella enterica is an L-threonine kinase used for
RT coenzyme B12 synthesis.";
RL J. Biol. Chem. 283:11322-11329(2008).
RN [5]
RP FUNCTION, CATALYTIC ACTIVITY, REACTION MECHANISM, AND MUTAGENESIS OF
RP GLU-24; SER-99; SER-100; THR-101; ASP-103; GLU-132; THR-134; ASP-135;
RP SER-253 AND SER-255.
RC STRAIN=LT2 / SGSC1412 / ATCC 700720;
RX PubMed=19509296; DOI=10.1074/jbc.m109.027425;
RA Fan C., Fromm H.J., Bobik T.A.;
RT "Kinetic and functional analysis of L-threonine kinase, the PduX enzyme of
RT Salmonella enterica.";
RL J. Biol. Chem. 284:20240-20248(2009).
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).
CC -!- FUNCTION: L-threonine kinase that catalyzes the conversion of L-
CC threonine to L-threonine-O-3-phosphate. Involved in the de novo
CC synthesis of adenosylcobalamin (coenzyme B12) and the assimilation of
CC cobyric acid. Uses ATP; the activity with CTP, GTP or UTP is 6, 11, and
CC 3% of the activity with ATP, respectively.
CC {ECO:0000269|PubMed:18308727, ECO:0000269|PubMed:19509296}.
CC -!- FUNCTION: The 1,2-propanediol (1,2-PD)-specific bacterial
CC microcompartment (BMC) concentrates low levels of 1,2-PD catabolic
CC enzymes, concentrates volatile reaction intermediates thus enhancing
CC pathway flux and keeps the level of toxic, mutagenic propionaldehyde
CC low. This gene probably benefits from its induction via the Pdu
CC promoter, rather than a physical interaction with the BMC.
CC {ECO:0000305|PubMed:28475631}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + L-threonine = ADP + H(+) + O-phospho-L-threonine;
CC Xref=Rhea:RHEA:33707, ChEBI:CHEBI:15378, ChEBI:CHEBI:30616,
CC ChEBI:CHEBI:57926, ChEBI:CHEBI:58675, ChEBI:CHEBI:456216;
CC EC=2.7.1.177; Evidence={ECO:0000269|PubMed:18308727,
CC ECO:0000269|PubMed:19509296};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=54.7 uM for ATP {ECO:0000269|PubMed:18308727};
CC KM=146.1 uM for L-threonine {ECO:0000269|PubMed:18308727};
CC Vmax=62.1 nmol/min/mg enzyme {ECO:0000269|PubMed:18308727};
CC -!- PATHWAY: Cofactor biosynthesis; adenosylcobalamin biosynthesis.
CC {ECO:0000305|PubMed:18308727}.
CC -!- PATHWAY: Polyol metabolism; 1,2-propanediol degradation.
CC {ECO:0000305|PubMed:10498708}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000305}.
CC -!- INDUCTION: The BMC operon and BMC production is induced by growth on
CC 1,2-PD vitamin B12 medium. {ECO:0000269|PubMed:10498708}.
CC -!- DISRUPTION PHENOTYPE: Growth is impaired on 1,2-PD minimal medium
CC supplemented with cobyric acid, but is restored on similar medium
CC supplemented with vitamin B12, cobinamide (PubMed:18308727). A double
CC pduW-pduX deletion grows as well as wild-type on 1,2-PD
CC (PubMed:12700259). {ECO:0000269|PubMed:12700259,
CC ECO:0000269|PubMed:18308727}.
CC -!- MISCELLANEOUS: Catalysis proceeds by a steady-state ordered bi-bi
CC complex mechanism in which ATP is the first substrate to bind.
CC {ECO:0000305|PubMed:19509296}.
CC -!- SIMILARITY: Belongs to the GHMP kinase family. PduX subfamily.
CC {ECO:0000305}.
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DR EMBL; AF026270; AAD39022.1; -; Genomic_DNA.
DR EMBL; AE006468; AAL20962.1; -; Genomic_DNA.
DR RefSeq; NP_461003.1; NC_003197.2.
DR RefSeq; WP_001201306.1; NC_003197.2.
DR AlphaFoldDB; Q9XDM4; -.
DR SMR; Q9XDM4; -.
DR STRING; 99287.STM2058; -.
DR PaxDb; Q9XDM4; -.
DR EnsemblBacteria; AAL20962; AAL20962; STM2058.
DR GeneID; 1253579; -.
DR KEGG; stm:STM2058; -.
DR PATRIC; fig|99287.12.peg.2180; -.
DR HOGENOM; CLU_056896_0_0_6; -.
DR OMA; DWYSTVE; -.
DR PhylomeDB; Q9XDM4; -.
DR BioCyc; MetaCyc:MON-13230; -.
DR BioCyc; SENT99287:STM2058-MON; -.
DR BRENDA; 2.7.1.177; 2169.
DR SABIO-RK; Q9XDM4; -.
DR UniPathway; UPA00148; -.
DR UniPathway; UPA00621; -.
DR Proteomes; UP000001014; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0016301; F:kinase activity; IDA:UniProtKB.
DR GO; GO:0009236; P:cobalamin biosynthetic process; IMP:UniProtKB.
DR GO; GO:0016310; P:phosphorylation; IEA:UniProtKB-KW.
DR GO; GO:0051144; P:propanediol catabolic process; IEA:UniProtKB-UniPathway.
DR Gene3D; 3.30.230.10; -; 1.
DR InterPro; IPR006204; GHMP_kinase_N_dom.
DR InterPro; IPR012363; PduX.
DR InterPro; IPR020568; Ribosomal_S5_D2-typ_fold.
DR InterPro; IPR014721; Ribosomal_S5_D2-typ_fold_subgr.
DR PANTHER; PTHR43527:SF1; PTHR43527:SF1; 1.
DR Pfam; PF00288; GHMP_kinases_N; 1.
DR PIRSF; PIRSF033887; PduX; 1.
DR SUPFAM; SSF54211; SSF54211; 1.
PE 1: Evidence at protein level;
KW ATP-binding; Cobalamin biosynthesis; Cytoplasm; Kinase; Nucleotide-binding;
KW Reference proteome; Transferase.
FT CHAIN 1..300
FT /note="L-threonine kinase"
FT /id="PRO_0000421736"
FT BINDING 92..102
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255"
FT MUTAGEN 24
FT /note="E->A: Impaired helical structure and abolished
FT catalytic activity."
FT /evidence="ECO:0000269|PubMed:19509296"
FT MUTAGEN 24
FT /note="E->Q: Does not affect catalytic activity."
FT /evidence="ECO:0000269|PubMed:19509296"
FT MUTAGEN 99
FT /note="S->A: Increased KM for ATP."
FT /evidence="ECO:0000269|PubMed:19509296"
FT MUTAGEN 100
FT /note="S->A: Abolished catalytic activity."
FT /evidence="ECO:0000269|PubMed:19509296"
FT MUTAGEN 101
FT /note="T->A: Does not affect catalytic activity."
FT /evidence="ECO:0000269|PubMed:19509296"
FT MUTAGEN 103
FT /note="D->A: Does not affect catalytic activity."
FT /evidence="ECO:0000269|PubMed:19509296"
FT MUTAGEN 103
FT /note="D->N: Does not affect catalytic activity."
FT /evidence="ECO:0000269|PubMed:19509296"
FT MUTAGEN 132
FT /note="E->A: Increased KM for ATP."
FT /evidence="ECO:0000269|PubMed:19509296"
FT MUTAGEN 132
FT /note="E->Q: Increased KM for ATP."
FT /evidence="ECO:0000269|PubMed:19509296"
FT MUTAGEN 134
FT /note="T->A: Does not affect catalytic activity."
FT /evidence="ECO:0000269|PubMed:19509296"
FT MUTAGEN 135
FT /note="D->A: Impaired helical structure and abolished
FT catalytic activity."
FT /evidence="ECO:0000269|PubMed:19509296"
FT MUTAGEN 135
FT /note="D->N: Does not affect catalytic activity."
FT /evidence="ECO:0000269|PubMed:19509296"
FT MUTAGEN 253
FT /note="S->A: Increased KM for L-threonine."
FT /evidence="ECO:0000269|PubMed:19509296"
FT MUTAGEN 255
FT /note="S->A: Increased KM for L-threonine."
FT /evidence="ECO:0000269|PubMed:19509296"
SQ SEQUENCE 300 AA; 32787 MW; 18CB37B92A50856B CRC64;
MRAHYSYLKG DNVAVAQCPA SCGELIQGWI LGSEKLVSCP VDWYSTVAVT AAPPLINERP
LSRAMVERVL AHWQYPAHWS NEIRVDVRSS IPVAKGMASS TADIAATAVA TAHHLGHSLD
ETTLAQLCVS IEPTDSTVFH QLTLFDHNNA ATQIACEPPP PIDLLVLESP VTLRTQDYHR
LPRQQKLIAS SATLQQAWNL VQEACITQNP LRLGEAATLS AIASQTLLPK PGFTALLSLV
EECDLYGLNV AHSGSVVGLM LDRKRHDIAR LKGKLAEKKL TRHWPKQHLL KMVTGGVKLQ
