PDXK_ECOLI
ID PDXK_ECOLI Reviewed; 283 AA.
AC P40191; P76964;
DT 01-FEB-1995, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1997, sequence version 2.
DT 03-AUG-2022, entry version 166.
DE RecName: Full=Pyridoxine/pyridoxal/pyridoxamine kinase {ECO:0000303|PubMed:8764513, ECO:0000303|PubMed:9537380};
DE Short=PN/PL/PM kinase {ECO:0000303|PubMed:8764513};
DE EC=2.7.1.35 {ECO:0000269|PubMed:15249053, ECO:0000269|PubMed:9537380};
DE AltName: Full=B6-vitamer kinase {ECO:0000303|PubMed:8764513};
DE AltName: Full=Pyridoxal kinase 1 {ECO:0000303|PubMed:15249053};
DE Short=PL kinase 1 {ECO:0000303|PubMed:15249053};
GN Name=pdxK; Synonyms=yfeI; OrderedLocusNames=b2418, JW2411;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=8764513; DOI=10.1111/j.1574-6968.1996.tb08368.x;
RA Yang Y., Zhao G., Winkler M.E.;
RT "Identification of the pdxK gene that encodes pyridoxine (vitamin B6)
RT kinase in Escherichia coli K-12.";
RL FEMS Microbiol. Lett. 141:89-95(1996).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=9205837; DOI=10.1093/dnares/4.2.91;
RA Yamamoto Y., Aiba H., Baba T., Hayashi K., Inada T., Isono K., Itoh T.,
RA Kimura S., Kitagawa M., Makino K., Miki T., Mitsuhashi N., Mizobuchi K.,
RA Mori H., Nakade S., Nakamura Y., Nashimoto H., Oshima T., Oyama S.,
RA Saito N., Sampei G., Satoh Y., Sivasundaram S., Tagami H., Takahashi H.,
RA Takeda J., Takemoto K., Uehara K., Wada C., Yamagata S., Horiuchi T.;
RT "Construction of a contiguous 874-kb sequence of the Escherichia coli-K12
RT genome corresponding to 50.0-68.8 min on the linkage map and analysis of
RT its sequence features.";
RL DNA Res. 4:91-113(1997).
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 NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 250-283.
RX PubMed=2457575; DOI=10.1128/jb.170.9.3827-3837.1988;
RA de Reuse H., Danchin A.;
RT "The ptsH, ptsI, and crr genes of the Escherichia coli phosphoenolpyruvate-
RT dependent phosphotransferase system: a complex operon with several modes of
RT transcription.";
RL J. Bacteriol. 170:3827-3837(1988).
RN [6]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 280-283.
RX PubMed=2960675; DOI=10.1016/s0021-9258(18)47721-6;
RA Saffen D.W., Presper K.A., Doering T.L., Roseman S.;
RT "Sugar transport by the bacterial phosphotransferase system. Molecular
RT cloning and structural analysis of the Escherichia coli ptsH, ptsI, and crr
RT genes.";
RL J. Biol. Chem. 262:16241-16253(1987).
RN [7]
RP FUNCTION, CATALYTIC ACTIVITY, DISRUPTION PHENOTYPE, AND PATHWAY.
RC STRAIN=K12;
RX PubMed=9537380; DOI=10.1128/jb.180.7.1814-1821.1998;
RA Yang Y., Tsui H.C., Man T.K., Winkler M.E.;
RT "Identification and function of the pdxY gene, which encodes a novel
RT pyridoxal kinase involved in the salvage pathway of pyridoxal 5'-phosphate
RT biosynthesis in Escherichia coli K-12.";
RL J. Bacteriol. 180:1814-1821(1998).
RN [8]
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, AND COFACTOR.
RX PubMed=15249053; DOI=10.1016/j.pep.2004.04.021;
RA di Salvo M.L., Hunt S., Schirch V.;
RT "Expression, purification, and kinetic constants for human and Escherichia
RT coli pyridoxal kinases.";
RL Protein Expr. Purif. 36:300-306(2004).
RN [9]
RP X-RAY CRYSTALLOGRAPHY (2.10 ANGSTROMS) OF APOENZYME AND IN COMPLEXES WITH
RP MG-ATP AND PYRIDOXAL, BIOPHYSICOCHEMICAL PROPERTIES, ACTIVITY REGULATION,
RP AND SUBUNIT.
RX PubMed=16740960; DOI=10.1128/jb.00122-06;
RA Safo M.K., Musayev F.N., di Salvo M.L., Hunt S., Claude J.B., Schirch V.;
RT "Crystal structure of pyridoxal kinase from the Escherichia coli pdxK gene:
RT implications for the classification of pyridoxal kinases.";
RL J. Bacteriol. 188:4542-4552(2006).
CC -!- FUNCTION: B6-vitamer kinase involved in the salvage pathway of
CC pyridoxal 5'-phosphate (PLP). Catalyzes the phosphorylation of
CC pyridoxine (PN), pyridoxal (PL), and pyridoxamine (PM), forming their
CC respective 5'-phosphorylated esters, i.e. PNP, PLP and PMP.
CC {ECO:0000269|PubMed:15249053, ECO:0000269|PubMed:9537380}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + pyridoxal = ADP + H(+) + pyridoxal 5'-phosphate;
CC Xref=Rhea:RHEA:10224, ChEBI:CHEBI:15378, ChEBI:CHEBI:17310,
CC ChEBI:CHEBI:30616, ChEBI:CHEBI:456216, ChEBI:CHEBI:597326;
CC EC=2.7.1.35; Evidence={ECO:0000269|PubMed:15249053,
CC ECO:0000269|PubMed:9537380};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + pyridoxine = ADP + H(+) + pyridoxine 5'-phosphate;
CC Xref=Rhea:RHEA:25108, ChEBI:CHEBI:15378, ChEBI:CHEBI:16709,
CC ChEBI:CHEBI:30616, ChEBI:CHEBI:58589, ChEBI:CHEBI:456216;
CC EC=2.7.1.35; Evidence={ECO:0000269|PubMed:15249053,
CC ECO:0000269|PubMed:9537380};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + pyridoxamine = ADP + H(+) + pyridoxamine 5'-phosphate;
CC Xref=Rhea:RHEA:25104, ChEBI:CHEBI:15378, ChEBI:CHEBI:30616,
CC ChEBI:CHEBI:57761, ChEBI:CHEBI:58451, ChEBI:CHEBI:456216;
CC EC=2.7.1.35; Evidence={ECO:0000269|PubMed:15249053};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000269|PubMed:15249053};
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:15249053};
CC Note=Can use both zinc and magnesium that is complexed with ATP.
CC However, magnesium seems to be the preferred metal used under
CC physiological conditions. {ECO:0000269|PubMed:15249053};
CC -!- ACTIVITY REGULATION: Is activated by the monovalent cation potassium.
CC {ECO:0000269|PubMed:16740960}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=100 uM for pyridoxal (in the presence of MgATP, at pH 7.3 and 37
CC degrees Celsius) {ECO:0000269|PubMed:15249053};
CC KM=50 uM for pyridoxal (in the presence of MgATP, at pH 7.3 and 37
CC degrees Celsius) {ECO:0000269|PubMed:16740960};
CC KM=190 uM for pyridoxal (in the presence of ZnATP, at pH 7.3 and 37
CC degrees Celsius) {ECO:0000269|PubMed:15249053};
CC KM=25 uM for pyridoxine (in the presence of MgATP, at pH 7.3 and 37
CC degrees Celsius) {ECO:0000269|PubMed:15249053};
CC KM=30 uM for pyridoxamine (in the presence of MgATP, at pH 7.3 and 37
CC degrees Celsius) {ECO:0000269|PubMed:15249053};
CC KM=10 uM for pyridoxamine (in the presence of ZnATP, at pH 7.3 and 37
CC degrees Celsius) {ECO:0000269|PubMed:15249053};
CC KM=600 uM for MgATP (at pH 7.3 and 37 degrees Celsius)
CC {ECO:0000269|PubMed:15249053};
CC KM=450 uM for MgATP (at pH 7.3 and 37 degrees Celsius)
CC {ECO:0000269|PubMed:16740960};
CC KM=2100 uM for MgATP (at pH 6.1 and 37 degrees Celsius)
CC {ECO:0000269|PubMed:15249053};
CC KM=70 uM for ZnATP (in the presence of pyridoxal, at pH 7.3 and 37
CC degrees Celsius) {ECO:0000269|PubMed:15249053};
CC KM=45 uM for ZnATP (in the presence of pyridoxamine, at pH 7.3 and 37
CC degrees Celsius) {ECO:0000269|PubMed:15249053};
CC Note=kcat is 140 min(-1) for the phosphorylation of PL with MgATP.
CC kcat is 120 min(-1) for the phosphorylation of PL with ZnATP. kcat is
CC 20 min(-1) for the phosphorylation of PN with MgATP. kcat is 40 min(-
CC 1) for the phosphorylation of PM with MgATP. kcat is 25 min(-1) for
CC the phosphorylation of PM with ZnATP (at pH 7.3 and 37 degrees
CC Celsius) (PubMed:15249053). kcat is 250 min(-1) for the
CC phosphorylation of PL with MgATP (at pH 7.3 and 37 degrees Celsius)
CC (PubMed:16740960). {ECO:0000269|PubMed:15249053,
CC ECO:0000269|PubMed:16740960};
CC -!- PATHWAY: Cofactor metabolism; pyridoxal 5'-phosphate salvage; pyridoxal
CC 5'-phosphate from pyridoxal: step 1/1. {ECO:0000269|PubMed:9537380}.
CC -!- PATHWAY: Cofactor metabolism; pyridoxal 5'-phosphate salvage;
CC pyridoxine 5'-phosphate from pyridoxine: step 1/1.
CC {ECO:0000269|PubMed:9537380}.
CC -!- PATHWAY: Cofactor metabolism; pyridoxal 5'-phosphate salvage;
CC pyridoxamine 5'-phosphate from pyridoxamine: step 1/1.
CC {ECO:0000305|PubMed:15249053}.
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:16740960}.
CC -!- DISRUPTION PHENOTYPE: Cells lacking this gene lack pyridoxine kinase
CC activity but still contain pyridoxal kinase activity (PubMed:8764513).
CC Cells lacking this gene and cells lacking both pdxY and pdxK are not
CC auxotrophs, meaning that the de novo pathway of PLP biosynthesis is
CC functional. For PLP salvage, the pdxY single mutant can use both
CC pyridoxine and pyridoxal, the pdxK single mutant can use pyridoxal but
CC not pyridoxine, and the double mutant can no longer use both compounds
CC (PubMed:9537380). {ECO:0000269|PubMed:8764513,
CC ECO:0000269|PubMed:9537380}.
CC -!- SIMILARITY: Belongs to the pyridoxine kinase family. PdxK subfamily.
CC {ECO:0000305}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; U53700; AAC44166.1; -; Genomic_DNA.
DR EMBL; U00096; AAC75471.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA16292.1; -; Genomic_DNA.
DR EMBL; M21994; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; J02796; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR PIR; A65016; A65016.
DR RefSeq; NP_416913.1; NC_000913.3.
DR RefSeq; WP_000096674.1; NZ_LN832404.1.
DR PDB; 2DDM; X-ray; 2.10 A; A/B=1-283.
DR PDB; 2DDO; X-ray; 2.60 A; A/B=1-283.
DR PDB; 2DDW; X-ray; 3.20 A; A/B=1-283.
DR PDBsum; 2DDM; -.
DR PDBsum; 2DDO; -.
DR PDBsum; 2DDW; -.
DR AlphaFoldDB; P40191; -.
DR SMR; P40191; -.
DR BioGRID; 4260568; 21.
DR BioGRID; 851221; 4.
DR IntAct; P40191; 6.
DR STRING; 511145.b2418; -.
DR jPOST; P40191; -.
DR PaxDb; P40191; -.
DR PRIDE; P40191; -.
DR EnsemblBacteria; AAC75471; AAC75471; b2418.
DR EnsemblBacteria; BAA16292; BAA16292; BAA16292.
DR GeneID; 946881; -.
DR KEGG; ecj:JW2411; -.
DR KEGG; eco:b2418; -.
DR PATRIC; fig|1411691.4.peg.4313; -.
DR EchoBASE; EB2519; -.
DR eggNOG; COG2240; Bacteria.
DR HOGENOM; CLU_046496_3_1_6; -.
DR InParanoid; P40191; -.
DR OMA; HVITHAR; -.
DR PhylomeDB; P40191; -.
DR BioCyc; EcoCyc:PDXK-MON; -.
DR BioCyc; MetaCyc:PDXK-MON; -.
DR BRENDA; 2.7.1.35; 2026.
DR UniPathway; UPA01068; UER00298.
DR UniPathway; UPA01068; UER00299.
DR UniPathway; UPA01068; UER00300.
DR EvolutionaryTrace; P40191; -.
DR PRO; PR:P40191; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR GO; GO:0008902; F:hydroxymethylpyrimidine kinase activity; IMP:EcoCyc.
DR GO; GO:0000287; F:magnesium ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0046872; F:metal ion binding; IDA:EcoCyc.
DR GO; GO:0030955; F:potassium ion binding; IDA:EcoCyc.
DR GO; GO:0008478; F:pyridoxal kinase activity; IDA:EcoCyc.
DR GO; GO:0030170; F:pyridoxal phosphate binding; IDA:EcoCyc.
DR GO; GO:0008270; F:zinc ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0016310; P:phosphorylation; IEA:UniProtKB-KW.
DR GO; GO:0009443; P:pyridoxal 5'-phosphate salvage; IDA:EcoCyc.
DR GO; GO:0008615; P:pyridoxine biosynthetic process; IMP:EcoCyc.
DR CDD; cd01173; pyridoxal_pyridoxamine_kinase; 1.
DR Gene3D; 3.40.1190.20; -; 1.
DR HAMAP; MF_01638; PdxK; 1.
DR InterPro; IPR023479; PdxK.
DR InterPro; IPR013749; PM/HMP-P_kinase-1.
DR InterPro; IPR004625; PyrdxlKinase.
DR InterPro; IPR029056; Ribokinase-like.
DR PANTHER; PTHR10534; PTHR10534; 1.
DR Pfam; PF08543; Phos_pyr_kin; 1.
DR SUPFAM; SSF53613; SSF53613; 1.
DR TIGRFAMs; TIGR00687; pyridox_kin; 1.
PE 1: Evidence at protein level;
KW 3D-structure; ATP-binding; Kinase; Magnesium; Metal-binding;
KW Nucleotide-binding; Reference proteome; Transferase; Zinc.
FT CHAIN 1..283
FT /note="Pyridoxine/pyridoxal/pyridoxamine kinase"
FT /id="PRO_0000213342"
FT BINDING 23
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:16740960,
FT ECO:0007744|PDB:2DDW"
FT BINDING 59
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:16740960,
FT ECO:0007744|PDB:2DDW"
FT BINDING 125
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000269|PubMed:16740960,
FT ECO:0007744|PDB:2DDO"
FT BINDING 136
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000305|PubMed:16740960"
FT BINDING 157
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000269|PubMed:16740960,
FT ECO:0007744|PDB:2DDO"
FT BINDING 162
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000269|PubMed:16740960,
FT ECO:0007744|PDB:2DDO"
FT BINDING 162
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:16740960"
FT BINDING 195
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000269|PubMed:16740960,
FT ECO:0007744|PDB:2DDO"
FT BINDING 221..224
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000269|PubMed:16740960,
FT ECO:0007744|PDB:2DDO"
FT BINDING 231
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000269|PubMed:16740960,
FT ECO:0007744|PDB:2DDO"
FT BINDING 233
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:16740960,
FT ECO:0007744|PDB:2DDW"
FT STRAND 17..30
FT /evidence="ECO:0007829|PDB:2DDM"
FT HELIX 32..41
FT /evidence="ECO:0007829|PDB:2DDM"
FT STRAND 46..56
FT /evidence="ECO:0007829|PDB:2DDM"
FT STRAND 65..67
FT /evidence="ECO:0007829|PDB:2DDM"
FT HELIX 70..82
FT /evidence="ECO:0007829|PDB:2DDM"
FT STRAND 91..94
FT /evidence="ECO:0007829|PDB:2DDM"
FT HELIX 100..114
FT /evidence="ECO:0007829|PDB:2DDM"
FT STRAND 121..124
FT /evidence="ECO:0007829|PDB:2DDM"
FT TURN 131..133
FT /evidence="ECO:0007829|PDB:2DDM"
FT HELIX 141..147
FT /evidence="ECO:0007829|PDB:2DDM"
FT HELIX 150..152
FT /evidence="ECO:0007829|PDB:2DDM"
FT STRAND 154..156
FT /evidence="ECO:0007829|PDB:2DDM"
FT HELIX 160..167
FT /evidence="ECO:0007829|PDB:2DDM"
FT HELIX 174..184
FT /evidence="ECO:0007829|PDB:2DDM"
FT STRAND 191..198
FT /evidence="ECO:0007829|PDB:2DDM"
FT STRAND 205..212
FT /evidence="ECO:0007829|PDB:2DDM"
FT STRAND 215..222
FT /evidence="ECO:0007829|PDB:2DDM"
FT HELIX 231..244
FT /evidence="ECO:0007829|PDB:2DDM"
FT HELIX 249..269
FT /evidence="ECO:0007829|PDB:2DDM"
SQ SEQUENCE 283 AA; 30847 MW; 8DFEDADD2F589EA0 CRC64;
MSSLLLFNDK SRALQADIVA VQSQVVYGSV GNSIAVPAIK QNGLNVFAVP TVLLSNTPHY
DTFYGGAIPD EWFSGYLRAL QERDALRQLR AVTTGYMGTA SQIKILAEWL TALRKDHPDL
LIMVDPVIGD IDSGIYVKPD LPEAYRQYLL PLAQGITPNI FELEILTGKN CRDLDSAIAA
AKSLLSDTLK WVVVTSASGN EENQEMQVVV VTADSVNVIS HSRVKTDLKG TGDLFCAQLI
SGLLKGKALT DAVHRAGLRV LEVMRYTQQH ESDELILPPL AEA
