PDXA_ECOLI
ID PDXA_ECOLI Reviewed; 329 AA.
AC P19624;
DT 01-FEB-1991, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-1991, sequence version 1.
DT 03-AUG-2022, entry version 182.
DE RecName: Full=4-hydroxythreonine-4-phosphate dehydrogenase {ECO:0000255|HAMAP-Rule:MF_00536};
DE EC=1.1.1.262 {ECO:0000255|HAMAP-Rule:MF_00536, ECO:0000269|PubMed:15026039};
DE AltName: Full=4-(phosphohydroxy)-L-threonine dehydrogenase {ECO:0000255|HAMAP-Rule:MF_00536};
GN Name=pdxA; OrderedLocusNames=b0052, JW0051;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K12;
RX PubMed=2670894; DOI=10.1128/jb.171.9.4767-4777.1989;
RA Roa B.B., Connolly D.M., Winkler M.E.;
RT "Overlap between pdxA and ksgA in the complex pdxA-ksgA-apaG-apaH operon of
RT Escherichia coli K-12.";
RL J. Bacteriol. 171:4767-4777(1989).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12;
RX PubMed=1630901; DOI=10.1093/nar/20.13.3305;
RA Yura T., Mori H., Nagai H., Nagata T., Ishihama A., Fujita N., Isono K.,
RA Mizobuchi K., Nakata A.;
RT "Systematic sequencing of the Escherichia coli genome: analysis of the 0-
RT 2.4 min region.";
RL Nucleic Acids Res. 20:3305-3308(1992).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [5]
RP FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES, AND COFACTOR.
RX DOI=10.1021/ja9742085;
RA Cane D.E., Hsiung Y., Cornish J.A., Robinson J.K., Spenser I.D.;
RT "Biosynthesis of vitamin B6: the oxidation of 4-hydroxy-L-threonine 4-
RT phosphate by pdxA.";
RL J. Am. Chem. Soc. 120:1936-1937(1998).
RN [6]
RP FUNCTION, AND CATALYTIC ACTIVITY.
RX PubMed=15026039; DOI=10.1016/j.bmcl.2004.01.065;
RA Banks J., Cane D.E.;
RT "Biosynthesis of vitamin B6: direct identification of the product of the
RT PdxA-catalyzed oxidation of 4-hydroxy-L-threonine-4-phosphate using
RT electrospray ionization mass spectrometry.";
RL Bioorg. Med. Chem. Lett. 14:1633-1636(2004).
RN [7]
RP X-RAY CRYSTALLOGRAPHY (1.96 ANGSTROMS) IN COMPLEX WITH SUBSTRATE AND ZINC
RP IONS, COFACTOR, AND SUBUNIT.
RX PubMed=12896974; DOI=10.1074/jbc.m306344200;
RA Sivaraman J., Li Y., Banks J., Cane D.E., Matte A., Cygler M.;
RT "Crystal structure of Escherichia coli PdxA, an enzyme involved in the
RT pyridoxal phosphate biosynthesis pathway.";
RL J. Biol. Chem. 278:43682-43690(2003).
CC -!- FUNCTION: Catalyzes the NAD(P)-dependent oxidation of 4-(phosphooxy)-L-
CC threonine (HTP) into 2-amino-3-oxo-4-(phosphooxy)butyric acid which
CC spontaneously decarboxylates to form 3-amino-2-oxopropyl phosphate
CC (AHAP). {ECO:0000255|HAMAP-Rule:MF_00536, ECO:0000269|PubMed:15026039,
CC ECO:0000269|Ref.5}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=4-(phosphooxy)-L-threonine + NAD(+) = 3-amino-2-oxopropyl
CC phosphate + CO2 + NADH; Xref=Rhea:RHEA:32275, ChEBI:CHEBI:16526,
CC ChEBI:CHEBI:57279, ChEBI:CHEBI:57540, ChEBI:CHEBI:57945,
CC ChEBI:CHEBI:58452; EC=1.1.1.262; Evidence={ECO:0000255|HAMAP-
CC Rule:MF_00536, ECO:0000269|PubMed:15026039};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00536,
CC ECO:0000269|PubMed:12896974, ECO:0000269|Ref.5};
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00536,
CC ECO:0000269|PubMed:12896974, ECO:0000269|Ref.5};
CC Name=Co(2+); Xref=ChEBI:CHEBI:48828;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00536,
CC ECO:0000269|PubMed:12896974, ECO:0000269|Ref.5};
CC Note=Binds 1 divalent metal cation per subunit. Can use ions such as
CC Zn(2+), Mg(2+) or Co(2+). {ECO:0000255|HAMAP-Rule:MF_00536,
CC ECO:0000269|PubMed:12896974, ECO:0000269|Ref.5};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=85 uM for 4-(phosphooxy)-L-threonine (at 0.1 M Tris-HCl and pH
CC 7.5) {ECO:0000269|Ref.5};
CC KM=113 uM for 4-(phosphooxy)-L-threonine (at 0.1 M phosphate buffer
CC and pH 7.5) {ECO:0000269|Ref.5};
CC Vmax=2.8 umol/min/mg enzyme with 4-(phosphooxy)-L-threonine as
CC substrate (at 0.1 M Tris-HCl and pH 7.5) {ECO:0000269|Ref.5};
CC Vmax=0.66 umol/min/mg enzyme with 4-(phosphooxy)-L-threonine as
CC substrate (at 0.1 M phosphate buffer and pH 7.5) {ECO:0000269|Ref.5};
CC -!- PATHWAY: Cofactor biosynthesis; pyridoxine 5'-phosphate biosynthesis;
CC pyridoxine 5'-phosphate from D-erythrose 4-phosphate: step 4/5.
CC {ECO:0000255|HAMAP-Rule:MF_00536}.
CC -!- SUBUNIT: Homodimer. {ECO:0000255|HAMAP-Rule:MF_00536,
CC ECO:0000269|PubMed:12896974}.
CC -!- INTERACTION:
CC P19624; P19624: pdxA; NbExp=3; IntAct=EBI-1112869, EBI-1112869;
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00536}.
CC -!- MISCELLANEOUS: The active site is located at the dimer interface.
CC {ECO:0000255|HAMAP-Rule:MF_00536, ECO:0000269|PubMed:12896974}.
CC -!- MISCELLANEOUS: According to PubMed:15026039, PdxA may catalyze both
CC oxidation and decarboxylation reactions that directly lead to AHAP.
CC -!- SIMILARITY: Belongs to the PdxA family. {ECO:0000255|HAMAP-
CC Rule:MF_00536, ECO:0000305}.
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DR EMBL; M68521; AAA24305.1; -; Genomic_DNA.
DR EMBL; U00096; AAC73163.1; -; Genomic_DNA.
DR EMBL; AP009048; BAB96619.1; -; Genomic_DNA.
DR PIR; JV0026; BVECXA.
DR RefSeq; NP_414594.1; NC_000913.3.
DR RefSeq; WP_000241277.1; NZ_STEB01000010.1.
DR PDB; 1PS6; X-ray; 2.25 A; A/B=2-329.
DR PDB; 1PS7; X-ray; 2.47 A; A/B/C/D=1-329.
DR PDB; 1PTM; X-ray; 1.96 A; A/B=1-329.
DR PDBsum; 1PS6; -.
DR PDBsum; 1PS7; -.
DR PDBsum; 1PTM; -.
DR AlphaFoldDB; P19624; -.
DR SMR; P19624; -.
DR BioGRID; 4261013; 7.
DR BioGRID; 849317; 5.
DR DIP; DIP-10448N; -.
DR IntAct; P19624; 5.
DR STRING; 511145.b0052; -.
DR DrugBank; DB02609; 4-Hydroxy-L-Threonine-5-Monophosphate.
DR jPOST; P19624; -.
DR PaxDb; P19624; -.
DR PRIDE; P19624; -.
DR EnsemblBacteria; AAC73163; AAC73163; b0052.
DR EnsemblBacteria; BAB96619; BAB96619; BAB96619.
DR GeneID; 944919; -.
DR KEGG; ecj:JW0051; -.
DR KEGG; eco:b0052; -.
DR PATRIC; fig|1411691.4.peg.2231; -.
DR EchoBASE; EB0685; -.
DR eggNOG; COG1995; Bacteria.
DR HOGENOM; CLU_040168_1_0_6; -.
DR InParanoid; P19624; -.
DR OMA; TAQVVMM; -.
DR PhylomeDB; P19624; -.
DR BioCyc; EcoCyc:PDXA-MON; -.
DR BioCyc; MetaCyc:PDXA-MON; -.
DR BRENDA; 1.1.1.262; 2026.
DR UniPathway; UPA00244; UER00312.
DR EvolutionaryTrace; P19624; -.
DR PRO; PR:P19624; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0050570; F:4-hydroxythreonine-4-phosphate dehydrogenase activity; IDA:EcoCyc.
DR GO; GO:0050897; F:cobalt ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0042802; F:identical protein binding; IPI:IntAct.
DR GO; GO:0000287; F:magnesium ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0051287; F:NAD binding; IEA:InterPro.
DR GO; GO:0008270; F:zinc ion binding; IDA:EcoCyc.
DR GO; GO:0042823; P:pyridoxal phosphate biosynthetic process; IMP:EcoCyc.
DR GO; GO:0008615; P:pyridoxine biosynthetic process; IMP:EcoCyc.
DR HAMAP; MF_00536; PdxA; 1.
DR InterPro; IPR037510; PdxA.
DR InterPro; IPR005255; PdxA_fam.
DR PANTHER; PTHR30004; PTHR30004; 1.
DR Pfam; PF04166; PdxA; 1.
DR TIGRFAMs; TIGR00557; pdxA; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cobalt; Cytoplasm; Magnesium; Metal-binding; NAD; NADP;
KW Oxidoreductase; Pyridoxine biosynthesis; Reference proteome; Zinc.
FT CHAIN 1..329
FT /note="4-hydroxythreonine-4-phosphate dehydrogenase"
FT /id="PRO_0000188804"
FT BINDING 136
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00536,
FT ECO:0000269|PubMed:12896974"
FT BINDING 137
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00536,
FT ECO:0000269|PubMed:12896974"
FT BINDING 166
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_note="ligand shared between dimeric partners"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00536,
FT ECO:0000305|PubMed:12896974"
FT BINDING 211
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_note="ligand shared between dimeric partners"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00536,
FT ECO:0000305|PubMed:12896974"
FT BINDING 266
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_note="ligand shared between dimeric partners"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00536,
FT ECO:0000305|PubMed:12896974"
FT BINDING 274
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00536,
FT ECO:0000269|PubMed:12896974"
FT BINDING 283
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00536,
FT ECO:0000269|PubMed:12896974"
FT BINDING 292
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00536,
FT ECO:0000269|PubMed:12896974"
FT STRAND 6..10
FT /evidence="ECO:0007829|PDB:1PTM"
FT HELIX 18..25
FT /evidence="ECO:0007829|PDB:1PTM"
FT STRAND 31..38
FT /evidence="ECO:0007829|PDB:1PTM"
FT HELIX 40..49
FT /evidence="ECO:0007829|PDB:1PTM"
FT STRAND 55..58
FT /evidence="ECO:0007829|PDB:1PTM"
FT STRAND 72..77
FT /evidence="ECO:0007829|PDB:1PTM"
FT HELIX 93..109
FT /evidence="ECO:0007829|PDB:1PTM"
FT STRAND 114..118
FT /evidence="ECO:0007829|PDB:1PTM"
FT HELIX 123..128
FT /evidence="ECO:0007829|PDB:1PTM"
FT HELIX 136..143
FT /evidence="ECO:0007829|PDB:1PTM"
FT STRAND 150..157
FT /evidence="ECO:0007829|PDB:1PTM"
FT STRAND 159..164
FT /evidence="ECO:0007829|PDB:1PTM"
FT HELIX 169..171
FT /evidence="ECO:0007829|PDB:1PTM"
FT HELIX 172..175
FT /evidence="ECO:0007829|PDB:1PTM"
FT HELIX 178..194
FT /evidence="ECO:0007829|PDB:1PTM"
FT STRAND 202..206
FT /evidence="ECO:0007829|PDB:1PTM"
FT HELIX 210..216
FT /evidence="ECO:0007829|PDB:1PTM"
FT HELIX 221..224
FT /evidence="ECO:0007829|PDB:1PTM"
FT HELIX 226..235
FT /evidence="ECO:0007829|PDB:1PTM"
FT STRAND 239..244
FT /evidence="ECO:0007829|PDB:1PTM"
FT HELIX 246..249
FT /evidence="ECO:0007829|PDB:1PTM"
FT HELIX 252..255
FT /evidence="ECO:0007829|PDB:1PTM"
FT STRAND 259..265
FT /evidence="ECO:0007829|PDB:1PTM"
FT HELIX 266..274
FT /evidence="ECO:0007829|PDB:1PTM"
FT STRAND 278..280
FT /evidence="ECO:0007829|PDB:1PTM"
FT STRAND 282..294
FT /evidence="ECO:0007829|PDB:1PTM"
FT HELIX 301..303
FT /evidence="ECO:0007829|PDB:1PTM"
FT TURN 304..306
FT /evidence="ECO:0007829|PDB:1PS7"
FT HELIX 312..328
FT /evidence="ECO:0007829|PDB:1PTM"
SQ SEQUENCE 329 AA; 35114 MW; 44E1FEE233C86233 CRC64;
MVKTQRVVIT PGEPAGIGPD LVVQLAQREW PVELVVCADA TLLTNRAAML GLPLTLRPYS
PNSPAQPQTA GTLTLLPVAL RAPVTAGQLA VENGHYVVET LARACDGCLN GEFAALITGP
VHKGVINDAG IPFTGHTEFF EERSQAKKVV MMLATEELRV ALATTHLPLR DIADAITPAL
LHEVIAILHH DLRTKFGIAE PRILVCGLNP HAGEGGHMGT EEIDTIIPVL NELRAQGMKL
NGPLPADTLF QPKYLDNADA VLAMYHDQGL PVLKYQGFGR GVNITLGLPF IRTSVDHGTA
LELAGRGKAD VGSFITALNL AIKMIVNTQ
