TDCB_SALTY
ID TDCB_SALTY Reviewed; 329 AA.
AC P11954;
DT 01-OCT-1989, integrated into UniProtKB/Swiss-Prot.
DT 13-DEC-2001, sequence version 2.
DT 03-AUG-2022, entry version 142.
DE RecName: Full=L-threonine dehydratase catabolic TdcB;
DE EC=4.3.1.19;
DE AltName: Full=L-serine dehydratase;
DE EC=4.3.1.17;
DE AltName: Full=Threonine deaminase;
GN Name=tdcB; OrderedLocusNames=STM3244;
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 [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 [2]
RP PROTEIN SEQUENCE OF 1-24.
RX PubMed=6751404; DOI=10.1016/0167-4838(82)90371-5;
RA Kim S.S., Datta P.;
RT "Chemical characterization of biodegradative threonine dehydratases from
RT two enteric bacteria.";
RL Biochim. Biophys. Acta 706:27-35(1982).
RN [3]
RP REVIEW.
RX PubMed=17954980; DOI=10.1007/s12038-007-0121-1;
RA Simanshu D.K., Chittori S., Savithri H.S., Murthy M.R.;
RT "Structure and function of enzymes involved in the anaerobic degradation of
RT L-threonine to propionate.";
RL J. Biosci. 32:1195-1206(2007).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) OF 2-329 IN COMPLEX WITH CMP AND
RP PYRIDOXAL PHOSPHATE, FUNCTION AS A THREONINE DEHYDRATASE,
RP BIOPHYSICOCHEMICAL PROPERTIES, AND SUBUNIT.
RX PubMed=17046821; DOI=10.1074/jbc.m605721200;
RA Simanshu D.K., Savithri H.S., Murthy M.R.;
RT "Crystal structures of Salmonella typhimurium biodegradative threonine
RT deaminase and its complex with CMP provide structural insights into ligand-
RT induced oligomerization and enzyme activation.";
RL J. Biol. Chem. 281:39630-39641(2006).
CC -!- FUNCTION: Catalyzes the anaerobic formation of alpha-ketobutyrate and
CC ammonia from threonine in a two-step reaction. The first step involved
CC a dehydration of threonine and a production of enamine intermediates
CC (aminocrotonate), which tautomerizes to its imine form (iminobutyrate).
CC Both intermediates are unstable and short-lived. The second step is the
CC nonenzymatic hydrolysis of the enamine/imine intermediates to form 2-
CC ketobutyrate and free ammonia. In the low water environment of the
CC cell, the second step is accelerated by RidA. TdcB also dehydrates
CC serine to yield pyruvate via analogous enamine/imine intermediates.
CC {ECO:0000269|PubMed:17046821}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=L-threonine = 2-oxobutanoate + NH4(+); Xref=Rhea:RHEA:22108,
CC ChEBI:CHEBI:16763, ChEBI:CHEBI:28938, ChEBI:CHEBI:57926; EC=4.3.1.19;
CC -!- CATALYTIC ACTIVITY:
CC Reaction=L-serine = NH4(+) + pyruvate; Xref=Rhea:RHEA:19169,
CC ChEBI:CHEBI:15361, ChEBI:CHEBI:28938, ChEBI:CHEBI:33384; EC=4.3.1.17;
CC -!- COFACTOR:
CC Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
CC -!- ACTIVITY REGULATION: Each protein molecule can bind up to four
CC molecules of AMP, which act as an allosteric activator to the enzyme.
CC The enzyme is inhibited by alpha-keto acids and other catabolites.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=16 mM for L-threonine (in the presence of 5 mM of AMP at 25
CC dregrees Celsius and at pH 8) {ECO:0000269|PubMed:17046821};
CC KM=32 mM for L-threonine (in the presence of 5 mM of CMP at 25
CC dregrees Celsius and at pH 8) {ECO:0000269|PubMed:17046821};
CC KM=123 mM for L-threonine (at 25 dregrees Celsius and at pH 8)
CC {ECO:0000269|PubMed:17046821};
CC -!- PATHWAY: Amino-acid degradation; L-threonine degradation via propanoate
CC pathway; propanoate from L-threonine: step 1/4.
CC -!- SUBUNIT: In the native structure, TdcB is in a dimeric form, whereas in
CC the TdcB-AMP complex, it exists in a tetrameric form (dimer of dimers).
CC {ECO:0000269|PubMed:17046821}.
CC -!- SIMILARITY: Belongs to the serine/threonine dehydratase family.
CC {ECO:0000305}.
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DR EMBL; AE006468; AAL22117.1; -; Genomic_DNA.
DR RefSeq; NP_462158.1; NC_003197.2.
DR RefSeq; WP_000548370.1; NC_003197.2.
DR PDB; 2GN0; X-ray; 1.70 A; A/B/C/D=2-329.
DR PDB; 2GN1; X-ray; 2.20 A; A/B=2-329.
DR PDB; 2GN2; X-ray; 2.50 A; A=2-329.
DR PDBsum; 2GN0; -.
DR PDBsum; 2GN1; -.
DR PDBsum; 2GN2; -.
DR AlphaFoldDB; P11954; -.
DR SMR; P11954; -.
DR STRING; 99287.STM3244; -.
DR PaxDb; P11954; -.
DR EnsemblBacteria; AAL22117; AAL22117; STM3244.
DR GeneID; 1254767; -.
DR KEGG; stm:STM3244; -.
DR PATRIC; fig|99287.12.peg.3440; -.
DR HOGENOM; CLU_021152_4_1_6; -.
DR OMA; LIHPFDH; -.
DR PhylomeDB; P11954; -.
DR BioCyc; SENT99287:STM3244-MON; -.
DR SABIO-RK; P11954; -.
DR UniPathway; UPA00052; UER00507.
DR EvolutionaryTrace; P11954; -.
DR Proteomes; UP000001014; Chromosome.
DR GO; GO:0003941; F:L-serine ammonia-lyase activity; IBA:GO_Central.
DR GO; GO:0004794; F:L-threonine ammonia-lyase activity; IBA:GO_Central.
DR GO; GO:0000166; F:nucleotide binding; IEA:UniProtKB-KW.
DR GO; GO:0030170; F:pyridoxal phosphate binding; IEA:InterPro.
DR GO; GO:0009097; P:isoleucine biosynthetic process; IBA:GO_Central.
DR GO; GO:0006565; P:L-serine catabolic process; IBA:GO_Central.
DR GO; GO:0070689; P:L-threonine catabolic process to propionate; IEA:UniProtKB-UniPathway.
DR GO; GO:0006567; P:threonine catabolic process; IBA:GO_Central.
DR Gene3D; 3.40.50.1100; -; 2.
DR InterPro; IPR001926; PLP-dep.
DR InterPro; IPR000634; Ser/Thr_deHydtase_PyrdxlP-BS.
DR InterPro; IPR005789; Thr_deHydtase_catblc.
DR InterPro; IPR036052; Trypto_synt_PLP_dependent.
DR Pfam; PF00291; PALP; 1.
DR SUPFAM; SSF53686; SSF53686; 1.
DR TIGRFAMs; TIGR01127; ilvA_1Cterm; 1.
DR PROSITE; PS00165; DEHYDRATASE_SER_THR; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Allosteric enzyme; Direct protein sequencing; Lyase;
KW Nucleotide-binding; Pyridoxal phosphate; Reference proteome.
FT CHAIN 1..329
FT /note="L-threonine dehydratase catabolic TdcB"
FT /id="PRO_0000185585"
FT BINDING 53..54
FT /ligand="AMP"
FT /ligand_id="ChEBI:CHEBI:456215"
FT BINDING 88
FT /ligand="AMP"
FT /ligand_id="ChEBI:CHEBI:456215"
FT BINDING 119..120
FT /ligand="AMP"
FT /ligand_id="ChEBI:CHEBI:456215"
FT BINDING 314
FT /ligand="AMP"
FT /ligand_id="ChEBI:CHEBI:456215"
FT MOD_RES 58
FT /note="N6-(pyridoxal phosphate)lysine"
FT CONFLICT 24
FT /note="K -> I (in Ref. 2; AA sequence)"
FT /evidence="ECO:0000305"
FT HELIX 2..6
FT /evidence="ECO:0007829|PDB:2GN0"
FT STRAND 7..9
FT /evidence="ECO:0007829|PDB:2GN0"
FT HELIX 11..21
FT /evidence="ECO:0007829|PDB:2GN0"
FT TURN 22..24
FT /evidence="ECO:0007829|PDB:2GN0"
FT HELIX 34..40
FT /evidence="ECO:0007829|PDB:2GN0"
FT STRAND 42..48
FT /evidence="ECO:0007829|PDB:2GN0"
FT HELIX 49..51
FT /evidence="ECO:0007829|PDB:2GN0"
FT HELIX 53..55
FT /evidence="ECO:0007829|PDB:2GN0"
FT HELIX 60..68
FT /evidence="ECO:0007829|PDB:2GN0"
FT HELIX 71..75
FT /evidence="ECO:0007829|PDB:2GN0"
FT STRAND 78..81
FT /evidence="ECO:0007829|PDB:2GN0"
FT HELIX 85..97
FT /evidence="ECO:0007829|PDB:2GN0"
FT STRAND 101..105
FT /evidence="ECO:0007829|PDB:2GN0"
FT HELIX 111..120
FT /evidence="ECO:0007829|PDB:2GN0"
FT STRAND 123..126
FT /evidence="ECO:0007829|PDB:2GN0"
FT HELIX 131..145
FT /evidence="ECO:0007829|PDB:2GN0"
FT STRAND 152..155
FT /evidence="ECO:0007829|PDB:2GN0"
FT HELIX 156..172
FT /evidence="ECO:0007829|PDB:2GN0"
FT STRAND 178..182
FT /evidence="ECO:0007829|PDB:2GN0"
FT STRAND 184..186
FT /evidence="ECO:0007829|PDB:2GN0"
FT HELIX 187..199
FT /evidence="ECO:0007829|PDB:2GN0"
FT STRAND 203..210
FT /evidence="ECO:0007829|PDB:2GN0"
FT HELIX 215..222
FT /evidence="ECO:0007829|PDB:2GN0"
FT HELIX 236..238
FT /evidence="ECO:0007829|PDB:2GN0"
FT HELIX 245..254
FT /evidence="ECO:0007829|PDB:2GN0"
FT STRAND 257..261
FT /evidence="ECO:0007829|PDB:2GN0"
FT HELIX 263..277
FT /evidence="ECO:0007829|PDB:2GN0"
FT HELIX 284..286
FT /evidence="ECO:0007829|PDB:2GN0"
FT HELIX 287..293
FT /evidence="ECO:0007829|PDB:2GN0"
FT TURN 294..297
FT /evidence="ECO:0007829|PDB:2GN0"
FT HELIX 298..301
FT /evidence="ECO:0007829|PDB:2GN0"
FT STRAND 304..310
FT /evidence="ECO:0007829|PDB:2GN0"
FT HELIX 317..324
FT /evidence="ECO:0007829|PDB:2GN0"
SQ SEQUENCE 329 AA; 35141 MW; C1C619B021DE817C CRC64;
MHITYDLPVA IEDILEAKKR LAGKIYKTGM PRSNYFSERC KGEIFLKFEN MQRTGSFKIR
GAFNKLSSLT EAEKRKGVVA CSAGNHAQGV SLSCAMLGID GKVVMPKGAP KSKVAATCDY
SAEVVLHGDN FNDTIAKVSE IVETEGRIFI PPYDDPKVIA GQGTIGLEIM EDLYDVDNVI
VPIGGGGLIA GIAIAIKSIN PTIKVIGVQA ENVHGMAASY YTGEITTHRT TGTLADGCDV
SRPGNLTYEI VRELVDDIVL VSEDEIRNSM IALIQRNKVI TEGAGALACA ALLSGKLDSH
IQNRKTVSII SGGNIDLSRV SQITGLVDA
