COBD_SALTY
ID COBD_SALTY Reviewed; 364 AA.
AC P97084; Q8ZQZ9;
DT 19-JUL-2003, integrated into UniProtKB/Swiss-Prot.
DT 19-JUL-2003, sequence version 2.
DT 03-AUG-2022, entry version 132.
DE RecName: Full=Threonine-phosphate decarboxylase;
DE EC=4.1.1.81 {ECO:0000269|PubMed:9446573};
DE AltName: Full=L-threonine-O-3-phosphate decarboxylase;
GN Name=cobD; OrderedLocusNames=STM0644;
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, AND CATALYTIC ACTIVITY.
RC STRAIN=LT2;
RX PubMed=9446573; DOI=10.1074/jbc.273.5.2684;
RA Brushaber K.R., O'Toole G.A., Escalante-Semerena J.C.;
RT "CobD, a novel enzyme with L-threonine-O-3-phosphate decarboxylase
RT activity, is responsible for the synthesis of (R)-1-amino-2-propanol O-2-
RT phosphate, a proposed new intermediate in cobalamin biosynthesis in
RT Salmonella typhimurium LT2.";
RL J. Biol. Chem. 273:2684-2691(1998).
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] {ECO:0007744|PDB:1LKC}
RP X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) IN COMPLEX WITH PHOSPHATE AND
RP PYRIDOXAL PHOSPHATE, COFACTOR, AND SUBUNIT.
RX PubMed=11939774; DOI=10.1021/bi012111w;
RA Cheong C.-G., Bauer C.B., Brushaber K.R., Escalante-Semerena J.C.,
RA Rayment I.;
RT "Three-dimensional structure of the L-threonine-O-3-phosphate decarboxylase
RT (CobD) enzyme from Salmonella enterica.";
RL Biochemistry 41:4798-4808(2002).
RN [4] {ECO:0007744|PDB:1LC5, ECO:0007744|PDB:1LC7, ECO:0007744|PDB:1LC8}
RP X-RAY CRYSTALLOGRAPHY (1.46 ANGSTROMS) IN COMPLEXES WITH PHOSPHOTHREONINE
RP AND REACTION INTERMEDIATE, SUBUNIT, AND MASS SPECTROMETRY.
RX PubMed=12119022; DOI=10.1021/bi020294w;
RA Cheong C.-G., Escalante-Semerena J.C., Rayment I.;
RT "Structural studies of the L-threonine-O-3-phosphate decarboxylase (CobD)
RT enzyme from Salmonella enterica: the apo, substrate, and product-aldimine
RT complexes.";
RL Biochemistry 41:9079-9089(2002).
CC -!- FUNCTION: Decarboxylates L-threonine-O-3-phosphate to yield (R)-1-
CC amino-2-propanol O-2-phosphate, the precursor for the linkage between
CC the nucleotide loop and the corrin ring in cobalamin.
CC {ECO:0000269|PubMed:9446573}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H(+) + O-phospho-L-threonine = (R)-1-aminopropan-2-yl
CC phosphate + CO2; Xref=Rhea:RHEA:11492, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:16526, ChEBI:CHEBI:58563, ChEBI:CHEBI:58675; EC=4.1.1.81;
CC Evidence={ECO:0000269|PubMed:9446573};
CC -!- COFACTOR:
CC Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
CC Evidence={ECO:0000269|PubMed:11939774};
CC -!- PATHWAY: Cofactor biosynthesis; adenosylcobalamin biosynthesis.
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:11939774,
CC ECO:0000269|PubMed:12119022}.
CC -!- MASS SPECTROMETRY: Mass=40666; Method=Electrospray;
CC Evidence={ECO:0000269|PubMed:12119022};
CC -!- MASS SPECTROMETRY: Mass=40894; Method=Electrospray; Note=With pyridoxal
CC phosphate.; Evidence={ECO:0000269|PubMed:12119022};
CC -!- SIMILARITY: Belongs to the class-II pyridoxal-phosphate-dependent
CC aminotransferase family. {ECO:0000305}.
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DR EMBL; U90625; AAC79515.1; -; Genomic_DNA.
DR EMBL; AE006468; AAL19595.1; -; Genomic_DNA.
DR RefSeq; NP_459636.1; NC_003197.2.
DR RefSeq; WP_001173255.1; NC_003197.2.
DR PDB; 1LC5; X-ray; 1.46 A; A=1-364.
DR PDB; 1LC7; X-ray; 1.80 A; A=1-364.
DR PDB; 1LC8; X-ray; 1.80 A; A=1-364.
DR PDB; 1LKC; X-ray; 1.80 A; A=1-364.
DR PDBsum; 1LC5; -.
DR PDBsum; 1LC7; -.
DR PDBsum; 1LC8; -.
DR PDBsum; 1LKC; -.
DR AlphaFoldDB; P97084; -.
DR SMR; P97084; -.
DR STRING; 99287.STM0644; -.
DR DrugBank; DB02482; Phosphonothreonine.
DR DrugBank; DB03433; {3-[(3-Hydroxy-2-Methyl-5-Phosphonooxymethyl-Pyridin-4-Ylmethyl)-Amino]-2-Methyl-Propyl}-Phosphonic Acid.
DR PaxDb; P97084; -.
DR EnsemblBacteria; AAL19595; AAL19595; STM0644.
DR GeneID; 1252164; -.
DR KEGG; stm:STM0644; -.
DR PATRIC; fig|99287.12.peg.680; -.
DR HOGENOM; CLU_017584_3_2_6; -.
DR OMA; RDPWSVN; -.
DR PhylomeDB; P97084; -.
DR BioCyc; MetaCyc:MON-12856; -.
DR BioCyc; SENT99287:STM0644-MON; -.
DR BRENDA; 4.1.1.81; 5542.
DR UniPathway; UPA00148; -.
DR EvolutionaryTrace; P97084; -.
DR Proteomes; UP000001014; Chromosome.
DR GO; GO:0042802; F:identical protein binding; IDA:UniProtKB.
DR GO; GO:0042803; F:protein homodimerization activity; IDA:UniProtKB.
DR GO; GO:0030170; F:pyridoxal phosphate binding; IDA:UniProtKB.
DR GO; GO:0048472; F:threonine-phosphate decarboxylase activity; IDA:UniProtKB.
DR GO; GO:1901605; P:alpha-amino acid metabolic process; IEA:UniProt.
DR GO; GO:0009236; P:cobalamin biosynthetic process; IDA:UniProtKB.
DR Gene3D; 3.40.640.10; -; 1.
DR Gene3D; 3.90.1150.10; -; 1.
DR InterPro; IPR004839; Aminotransferase_I/II.
DR InterPro; IPR005860; CobD.
DR InterPro; IPR004838; NHTrfase_class1_PyrdxlP-BS.
DR InterPro; IPR015424; PyrdxlP-dep_Trfase.
DR InterPro; IPR015421; PyrdxlP-dep_Trfase_major.
DR InterPro; IPR015422; PyrdxlP-dep_Trfase_small.
DR Pfam; PF00155; Aminotran_1_2; 1.
DR SUPFAM; SSF53383; SSF53383; 1.
DR TIGRFAMs; TIGR01140; L_thr_O3P_dcar; 1.
DR PROSITE; PS00105; AA_TRANSFER_CLASS_1; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cobalamin biosynthesis; Lyase; Pyridoxal phosphate;
KW Reference proteome.
FT CHAIN 1..364
FT /note="Threonine-phosphate decarboxylase"
FT /id="PRO_0000163822"
FT BINDING 8..9
FT /ligand="O-phospho-L-threonine"
FT /ligand_id="ChEBI:CHEBI:58675"
FT /evidence="ECO:0000269|PubMed:12119022,
FT ECO:0007744|PDB:1LC7"
FT BINDING 32
FT /ligand="O-phospho-L-threonine"
FT /ligand_id="ChEBI:CHEBI:58675"
FT /evidence="ECO:0000269|PubMed:12119022,
FT ECO:0007744|PDB:1LC7"
FT BINDING 157
FT /ligand="O-phospho-L-threonine"
FT /ligand_id="ChEBI:CHEBI:58675"
FT /evidence="ECO:0000269|PubMed:12119022,
FT ECO:0007744|PDB:1LC7"
FT BINDING 323
FT /ligand="O-phospho-L-threonine"
FT /ligand_id="ChEBI:CHEBI:58675"
FT /evidence="ECO:0000269|PubMed:12119022,
FT ECO:0007744|PDB:1LC7"
FT BINDING 337
FT /ligand="O-phospho-L-threonine"
FT /ligand_id="ChEBI:CHEBI:58675"
FT /evidence="ECO:0000269|PubMed:12119022,
FT ECO:0007744|PDB:1LC7"
FT MOD_RES 216
FT /note="N6-(pyridoxal phosphate)lysine"
FT /evidence="ECO:0000269|PubMed:11939774,
FT ECO:0007744|PDB:1LKC"
FT CONFLICT 6
FT /note="S -> T (in Ref. 1; AAC79515)"
FT /evidence="ECO:0000305"
FT CONFLICT 15
FT /note="A -> P (in Ref. 1; AAC79515)"
FT /evidence="ECO:0000305"
FT CONFLICT 25
FT /note="Q -> H (in Ref. 1; AAC79515)"
FT /evidence="ECO:0000305"
FT CONFLICT 30
FT /note="S -> T (in Ref. 1; AAC79515)"
FT /evidence="ECO:0000305"
FT CONFLICT 42..45
FT /note="VKRA -> LKPP (in Ref. 1; AAC79515)"
FT /evidence="ECO:0000305"
FT STRAND 7..9
FT /evidence="ECO:0007829|PDB:1LC5"
FT HELIX 13..19
FT /evidence="ECO:0007829|PDB:1LC5"
FT HELIX 23..25
FT /evidence="ECO:0007829|PDB:1LC5"
FT STRAND 26..28
FT /evidence="ECO:0007829|PDB:1LC5"
FT HELIX 40..48
FT /evidence="ECO:0007829|PDB:1LC5"
FT HELIX 50..54
FT /evidence="ECO:0007829|PDB:1LC5"
FT HELIX 62..72
FT /evidence="ECO:0007829|PDB:1LC5"
FT HELIX 76..78
FT /evidence="ECO:0007829|PDB:1LC5"
FT STRAND 79..84
FT /evidence="ECO:0007829|PDB:1LC5"
FT HELIX 85..96
FT /evidence="ECO:0007829|PDB:1LC5"
FT STRAND 99..106
FT /evidence="ECO:0007829|PDB:1LC5"
FT HELIX 110..117
FT /evidence="ECO:0007829|PDB:1LC5"
FT STRAND 121..126
FT /evidence="ECO:0007829|PDB:1LC5"
FT HELIX 129..131
FT /evidence="ECO:0007829|PDB:1LC5"
FT HELIX 139..142
FT /evidence="ECO:0007829|PDB:1LC5"
FT STRAND 149..155
FT /evidence="ECO:0007829|PDB:1LC5"
FT TURN 157..159
FT /evidence="ECO:0007829|PDB:1LC5"
FT HELIX 165..178
FT /evidence="ECO:0007829|PDB:1LC5"
FT STRAND 181..185
FT /evidence="ECO:0007829|PDB:1LC5"
FT HELIX 189..191
FT /evidence="ECO:0007829|PDB:1LC5"
FT HELIX 199..201
FT /evidence="ECO:0007829|PDB:1LC5"
FT STRAND 208..214
FT /evidence="ECO:0007829|PDB:1LC5"
FT TURN 215..219
FT /evidence="ECO:0007829|PDB:1LC5"
FT TURN 221..223
FT /evidence="ECO:0007829|PDB:1LC5"
FT STRAND 226..229
FT /evidence="ECO:0007829|PDB:1LC5"
FT HELIX 233..242
FT /evidence="ECO:0007829|PDB:1LC5"
FT HELIX 250..258
FT /evidence="ECO:0007829|PDB:1LC5"
FT HELIX 259..261
FT /evidence="ECO:0007829|PDB:1LC5"
FT HELIX 263..285
FT /evidence="ECO:0007829|PDB:1LC5"
FT STRAND 290..292
FT /evidence="ECO:0007829|PDB:1LC5"
FT STRAND 296..305
FT /evidence="ECO:0007829|PDB:1LC5"
FT STRAND 306..308
FT /evidence="ECO:0007829|PDB:1LC7"
FT HELIX 311..316
FT /evidence="ECO:0007829|PDB:1LC5"
FT TURN 317..319
FT /evidence="ECO:0007829|PDB:1LC5"
FT STRAND 335..339
FT /evidence="ECO:0007829|PDB:1LC5"
FT HELIX 343..356
FT /evidence="ECO:0007829|PDB:1LC5"
SQ SEQUENCE 364 AA; 40766 MW; B6613FD0AB6D846C CRC64;
MALFNSAHGG NIREAATVLG ISPDQLLDFS ANINPLGMPV SVKRALIDNL DCIERYPDAD
YFHLHQALAR HHQVPASWIL AGNGETESIF TVASGLKPRR AMIVTPGFAE YGRALAQSGC
EIRRWSLREA DGWQLTDAIL EALTPDLDCL FLCTPNNPTG LLPERPLLQA IADRCKSLNI
NLILDEAFID FIPHETGFIP ALKDNPHIWV LRSLTKFYAI PGLRLGYLVN SDDAAMARMR
RQQMPWSVNA LAALAGEVAL QDSAWQQATW HWLREEGARF YQALCQLPLL TVYPGRANYL
LLRCEREDID LQRRLLTQRI LIRSCANYPG LDSRYYRVAI RSAAQNERLL AALRNVLTGI
APAD
