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Pyridoxine/pyridoxal/pyridoxamine kinase (PN/PL/PM kinase) (EC 2.7.1.35) (B6-vitamer kinase) (Pyridoxal kinase 1) (PL kinase 1)

 PDXK_ECOLI              Reviewed;         283 AA.
P40191; P76964;
01-FEB-1995, integrated into UniProtKB/Swiss-Prot.
01-NOV-1997, sequence version 2.
05-DEC-2018, entry version 147.
RecName: Full=Pyridoxine/pyridoxal/pyridoxamine kinase {ECO:0000303|PubMed:8764513, ECO:0000303|PubMed:9537380};
Short=PN/PL/PM kinase {ECO:0000303|PubMed:8764513};
EC=2.7.1.35 {ECO:0000269|PubMed:15249053, ECO:0000269|PubMed:9537380};
AltName: Full=B6-vitamer kinase {ECO:0000303|PubMed:8764513};
AltName: Full=Pyridoxal kinase 1 {ECO:0000303|PubMed:15249053};
Short=PL kinase 1 {ECO:0000303|PubMed:15249053};
Name=pdxK; Synonyms=yfeI; OrderedLocusNames=b2418, JW2411;
Escherichia coli (strain K12).
Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
Enterobacteriaceae; Escherichia.
NCBI_TaxID=83333;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, AND DISRUPTION PHENOTYPE.
STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
PubMed=8764513; DOI=10.1111/j.1574-6968.1996.tb08368.x;
Yang Y., Zhao G., Winkler M.E.;
"Identification of the pdxK gene that encodes pyridoxine (vitamin B6)
kinase in Escherichia coli K-12.";
FEMS Microbiol. Lett. 141:89-95(1996).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
PubMed=9205837; DOI=10.1093/dnares/4.2.91;
Yamamoto Y., Aiba H., Baba T., Hayashi K., Inada T., Isono K.,
Itoh T., Kimura S., Kitagawa M., Makino K., Miki T., Mitsuhashi N.,
Mizobuchi K., Mori H., Nakade S., Nakamura Y., Nashimoto H.,
Oshima T., Oyama S., Saito N., Sampei G., Satoh Y., Sivasundaram S.,
Tagami H., Takahashi H., Takeda J., Takemoto K., Uehara K., Wada C.,
Yamagata S., Horiuchi T.;
"Construction of a contiguous 874-kb sequence of the Escherichia coli-
K12 genome corresponding to 50.0-68.8 min on the linkage map and
analysis of its sequence features.";
DNA Res. 4:91-113(1997).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / MG1655 / ATCC 47076;
PubMed=9278503; DOI=10.1126/science.277.5331.1453;
Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J.,
Mau B., Shao Y.;
"The complete genome sequence of Escherichia coli K-12.";
Science 277:1453-1462(1997).
[4]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
PubMed=16738553; DOI=10.1038/msb4100049;
Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
"Highly accurate genome sequences of Escherichia coli K-12 strains
MG1655 and W3110.";
Mol. Syst. Biol. 2:E1-E5(2006).
[5]
NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 250-283.
PubMed=2457575;
de Reuse H., Danchin A.;
"The ptsH, ptsI, and crr genes of the Escherichia coli
phosphoenolpyruvate-dependent phosphotransferase system: a complex
operon with several modes of transcription.";
J. Bacteriol. 170:3827-3837(1988).
[6]
NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 280-283.
PubMed=2960675;
Saffen D.W., Presper K.A., Doering T.L., Roseman S.;
"Sugar transport by the bacterial phosphotransferase system. Molecular
cloning and structural analysis of the Escherichia coli ptsH, ptsI,
and crr genes.";
J. Biol. Chem. 262:16241-16253(1987).
[7]
FUNCTION, CATALYTIC ACTIVITY, DISRUPTION PHENOTYPE, AND PATHWAY.
STRAIN=K12;
PubMed=9537380;
Yang Y., Tsui H.C., Man T.K., Winkler M.E.;
"Identification and function of the pdxY gene, which encodes a novel
pyridoxal kinase involved in the salvage pathway of pyridoxal 5'-
phosphate biosynthesis in Escherichia coli K-12.";
J. Bacteriol. 180:1814-1821(1998).
[8]
FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, AND
COFACTOR.
PubMed=15249053; DOI=10.1016/j.pep.2004.04.021;
di Salvo M.L., Hunt S., Schirch V.;
"Expression, purification, and kinetic constants for human and
Escherichia coli pyridoxal kinases.";
Protein Expr. Purif. 36:300-306(2004).
[9]
X-RAY CRYSTALLOGRAPHY (2.10 ANGSTROMS) OF APOENZYME AND IN COMPLEXES
WITH MG-ATP AND PYRIDOXAL, BIOPHYSICOCHEMICAL PROPERTIES, ACTIVITY
REGULATION, AND SUBUNIT.
PubMed=16740960; DOI=10.1128/JB.00122-06;
Safo M.K., Musayev F.N., di Salvo M.L., Hunt S., Claude J.B.,
Schirch V.;
"Crystal structure of pyridoxal kinase from the Escherichia coli pdxK
gene: implications for the classification of pyridoxal kinases.";
J. Bacteriol. 188:4542-4552(2006).
-!- FUNCTION: B6-vitamer kinase involved in the salvage pathway of
pyridoxal 5'-phosphate (PLP). Catalyzes the phosphorylation of
pyridoxine (PN), pyridoxal (PL), and pyridoxamine (PM), forming
their respective 5'-phosphorylated esters, i.e. PNP, PLP and PMP.
{ECO:0000269|PubMed:15249053, ECO:0000269|PubMed:9537380}.
-!- CATALYTIC ACTIVITY:
Reaction=ATP + pyridoxal = ADP + H(+) + pyridoxal 5'-phosphate;
Xref=Rhea:RHEA:10224, ChEBI:CHEBI:15378, ChEBI:CHEBI:17310,
ChEBI:CHEBI:30616, ChEBI:CHEBI:456216, ChEBI:CHEBI:597326;
EC=2.7.1.35; Evidence={ECO:0000269|PubMed:15249053,
ECO:0000269|PubMed:9537380};
-!- CATALYTIC ACTIVITY:
Reaction=ATP + pyridoxine = ADP + H(+) + pyridoxine 5'-phosphate;
Xref=Rhea:RHEA:25108, ChEBI:CHEBI:15378, ChEBI:CHEBI:16709,
ChEBI:CHEBI:30616, ChEBI:CHEBI:58589, ChEBI:CHEBI:456216;
EC=2.7.1.35; Evidence={ECO:0000269|PubMed:15249053,
ECO:0000269|PubMed:9537380};
-!- CATALYTIC ACTIVITY:
Reaction=ATP + pyridoxamine = ADP + H(+) + pyridoxamine 5'-
phosphate; Xref=Rhea:RHEA:25104, ChEBI:CHEBI:15378,
ChEBI:CHEBI:30616, ChEBI:CHEBI:57761, ChEBI:CHEBI:58451,
ChEBI:CHEBI:456216; EC=2.7.1.35;
Evidence={ECO:0000269|PubMed:15249053};
-!- COFACTOR:
Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
Evidence={ECO:0000269|PubMed:15249053};
Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
Evidence={ECO:0000269|PubMed:15249053};
Note=Can use both zinc and magnesium that is complexed with ATP.
However, magnesium seems to be the preferred metal used under
physiological conditions. {ECO:0000269|PubMed:15249053};
-!- ACTIVITY REGULATION: Is activated by the monovalent cation
potassium. {ECO:0000269|PubMed:16740960}.
-!- BIOPHYSICOCHEMICAL PROPERTIES:
Kinetic parameters:
KM=100 uM for pyridoxal (in the presence of MgATP, at pH 7.3 and
37 degrees Celsius) {ECO:0000269|PubMed:15249053};
KM=50 uM for pyridoxal (in the presence of MgATP, at pH 7.3 and
37 degrees Celsius) {ECO:0000269|PubMed:16740960};
KM=190 uM for pyridoxal (in the presence of ZnATP, at pH 7.3 and
37 degrees Celsius) {ECO:0000269|PubMed:15249053};
KM=25 uM for pyridoxine (in the presence of MgATP, at pH 7.3 and
37 degrees Celsius) {ECO:0000269|PubMed:15249053};
KM=30 uM for pyridoxamine (in the presence of MgATP, at pH 7.3
and 37 degrees Celsius) {ECO:0000269|PubMed:15249053};
KM=10 uM for pyridoxamine (in the presence of ZnATP, at pH 7.3
and 37 degrees Celsius) {ECO:0000269|PubMed:15249053};
KM=600 uM for MgATP (at pH 7.3 and 37 degrees Celsius)
{ECO:0000269|PubMed:15249053};
KM=450 uM for MgATP (at pH 7.3 and 37 degrees Celsius)
{ECO:0000269|PubMed:16740960};
KM=2100 uM for MgATP (at pH 6.1 and 37 degrees Celsius)
{ECO:0000269|PubMed:15249053};
KM=70 uM for ZnATP (in the presence of pyridoxal, at pH 7.3 and
37 degrees Celsius) {ECO:0000269|PubMed:15249053};
KM=45 uM for ZnATP (in the presence of pyridoxamine, at pH 7.3
and 37 degrees Celsius) {ECO:0000269|PubMed:15249053};
Note=kcat is 140 min(-1) for the phosphorylation of PL with
MgATP. kcat is 120 min(-1) for the phosphorylation of PL with
ZnATP. kcat is 20 min(-1) for the phosphorylation of PN with
MgATP. kcat is 40 min(-1) for the phosphorylation of PM with
MgATP. kcat is 25 min(-1) for the phosphorylation of PM with
ZnATP (at pH 7.3 and 37 degrees Celsius) (PubMed:15249053). kcat
is 250 min(-1) for the phosphorylation of PL with MgATP (at pH
7.3 and 37 degrees Celsius) (PubMed:16740960).
{ECO:0000269|PubMed:15249053, ECO:0000269|PubMed:16740960};
-!- PATHWAY: Cofactor metabolism; pyridoxal 5'-phosphate salvage;
pyridoxal 5'-phosphate from pyridoxal: step 1/1.
{ECO:0000269|PubMed:9537380}.
-!- PATHWAY: Cofactor metabolism; pyridoxal 5'-phosphate salvage;
pyridoxine 5'-phosphate from pyridoxine: step 1/1.
{ECO:0000269|PubMed:9537380}.
-!- PATHWAY: Cofactor metabolism; pyridoxal 5'-phosphate salvage;
pyridoxamine 5'-phosphate from pyridoxamine: step 1/1.
{ECO:0000305|PubMed:15249053}.
-!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:16740960}.
-!- DISRUPTION PHENOTYPE: Cells lacking this gene lack pyridoxine
kinase activity but still contain pyridoxal kinase activity
(PubMed:8764513). Cells lacking this gene and cells lacking both
pdxY and pdxK are not auxotrophs, meaning that the de novo pathway
of PLP biosynthesis is functional. For PLP salvage, the pdxY
single mutant can use both pyridoxine and pyridoxal, the pdxK
single mutant can use pyridoxal but not pyridoxine, and the double
mutant can no longer use both compounds (PubMed:9537380).
{ECO:0000269|PubMed:8764513, ECO:0000269|PubMed:9537380}.
-!- SIMILARITY: Belongs to the pyridoxine kinase family. PdxK
subfamily. {ECO:0000305}.
-----------------------------------------------------------------------
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EMBL; U53700; AAC44166.1; -; Genomic_DNA.
EMBL; U00096; AAC75471.1; -; Genomic_DNA.
EMBL; AP009048; BAA16292.1; -; Genomic_DNA.
EMBL; M21994; -; NOT_ANNOTATED_CDS; Genomic_DNA.
EMBL; J02796; -; NOT_ANNOTATED_CDS; Genomic_DNA.
PIR; A65016; A65016.
RefSeq; NP_416913.1; NC_000913.3.
RefSeq; WP_000096674.1; NZ_LN832404.1.
PDB; 2DDM; X-ray; 2.10 A; A/B=1-283.
PDB; 2DDO; X-ray; 2.60 A; A/B=1-283.
PDB; 2DDW; X-ray; 3.20 A; A/B=1-283.
PDBsum; 2DDM; -.
PDBsum; 2DDO; -.
PDBsum; 2DDW; -.
ProteinModelPortal; P40191; -.
SMR; P40191; -.
BioGrid; 4260568; 21.
IntAct; P40191; 6.
STRING; 316385.ECDH10B_2583; -.
PaxDb; P40191; -.
PRIDE; P40191; -.
EnsemblBacteria; AAC75471; AAC75471; b2418.
EnsemblBacteria; BAA16292; BAA16292; BAA16292.
GeneID; 946881; -.
KEGG; ecj:JW2411; -.
KEGG; eco:b2418; -.
PATRIC; fig|1411691.4.peg.4313; -.
EchoBASE; EB2519; -.
EcoGene; EG12642; pdxK.
eggNOG; ENOG4107XGF; Bacteria.
eggNOG; COG2240; LUCA.
HOGENOM; HOG000258173; -.
InParanoid; P40191; -.
KO; K00868; -.
PhylomeDB; P40191; -.
BioCyc; EcoCyc:PDXK-MONOMER; -.
BioCyc; MetaCyc:PDXK-MONOMER; -.
BRENDA; 2.7.1.35; 2026.
UniPathway; UPA01068; UER00298.
UniPathway; UPA01068; UER00299.
UniPathway; UPA01068; UER00300.
EvolutionaryTrace; P40191; -.
PRO; PR:P40191; -.
Proteomes; UP000000318; Chromosome.
Proteomes; UP000000625; Chromosome.
GO; GO:0005829; C:cytosol; IDA:EcoCyc.
GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
GO; GO:0008902; F:hydroxymethylpyrimidine kinase activity; IMP:EcoCyc.
GO; GO:0000287; F:magnesium ion binding; IEA:UniProtKB-UniRule.
GO; GO:0046872; F:metal ion binding; IDA:EcoCyc.
GO; GO:0030955; F:potassium ion binding; IDA:EcoCyc.
GO; GO:0008478; F:pyridoxal kinase activity; IDA:EcoCyc.
GO; GO:0030170; F:pyridoxal phosphate binding; IDA:EcoCyc.
GO; GO:0008270; F:zinc ion binding; IEA:UniProtKB-UniRule.
GO; GO:0009443; P:pyridoxal 5'-phosphate salvage; IDA:EcoCyc.
GO; GO:0008615; P:pyridoxine biosynthetic process; IMP:EcoCyc.
CDD; cd01173; pyridoxal_pyridoxamine_kinase; 1.
Gene3D; 3.40.1190.20; -; 1.
HAMAP; MF_01638; PdxK; 1.
InterPro; IPR023479; PdxK.
InterPro; IPR013749; PM/HMP-P_kinase-1.
InterPro; IPR004625; PyrdxlKinase.
InterPro; IPR029056; Ribokinase-like.
PANTHER; PTHR10534; PTHR10534; 1.
Pfam; PF08543; Phos_pyr_kin; 1.
SUPFAM; SSF53613; SSF53613; 1.
TIGRFAMs; TIGR00687; pyridox_kin; 1.
1: Evidence at protein level;
3D-structure; ATP-binding; Complete proteome; Kinase; Magnesium;
Metal-binding; Nucleotide-binding; Reference proteome; Transferase;
Zinc.
CHAIN 1 283 Pyridoxine/pyridoxal/pyridoxamine kinase.
/FTId=PRO_0000213342.
NP_BIND 221 224 ATP. {ECO:0000244|PDB:2DDO,
ECO:0000269|PubMed:16740960}.
METAL 136 136 Magnesium. {ECO:0000305|PubMed:16740960}.
METAL 162 162 Magnesium. {ECO:0000269|PubMed:16740960}.
BINDING 23 23 Substrate. {ECO:0000244|PDB:2DDW,
ECO:0000269|PubMed:16740960}.
BINDING 59 59 Substrate. {ECO:0000244|PDB:2DDW,
ECO:0000269|PubMed:16740960}.
BINDING 125 125 ATP. {ECO:0000244|PDB:2DDO,
ECO:0000269|PubMed:16740960}.
BINDING 157 157 ATP; via carbonyl oxygen.
{ECO:0000244|PDB:2DDO,
ECO:0000269|PubMed:16740960}.
BINDING 162 162 ATP. {ECO:0000244|PDB:2DDO,
ECO:0000269|PubMed:16740960}.
BINDING 195 195 ATP. {ECO:0000244|PDB:2DDO,
ECO:0000269|PubMed:16740960}.
BINDING 231 231 ATP. {ECO:0000244|PDB:2DDO,
ECO:0000269|PubMed:16740960}.
BINDING 233 233 Substrate. {ECO:0000244|PDB:2DDW,
ECO:0000269|PubMed:16740960}.
STRAND 17 30 {ECO:0000244|PDB:2DDM}.
HELIX 32 41 {ECO:0000244|PDB:2DDM}.
STRAND 46 56 {ECO:0000244|PDB:2DDM}.
STRAND 65 67 {ECO:0000244|PDB:2DDM}.
HELIX 70 82 {ECO:0000244|PDB:2DDM}.
STRAND 91 94 {ECO:0000244|PDB:2DDM}.
HELIX 100 114 {ECO:0000244|PDB:2DDM}.
STRAND 121 124 {ECO:0000244|PDB:2DDM}.
TURN 131 133 {ECO:0000244|PDB:2DDM}.
HELIX 141 147 {ECO:0000244|PDB:2DDM}.
HELIX 150 152 {ECO:0000244|PDB:2DDM}.
STRAND 154 156 {ECO:0000244|PDB:2DDM}.
HELIX 160 167 {ECO:0000244|PDB:2DDM}.
HELIX 174 184 {ECO:0000244|PDB:2DDM}.
STRAND 191 198 {ECO:0000244|PDB:2DDM}.
STRAND 205 212 {ECO:0000244|PDB:2DDM}.
STRAND 215 222 {ECO:0000244|PDB:2DDM}.
HELIX 231 244 {ECO:0000244|PDB:2DDM}.
HELIX 249 269 {ECO:0000244|PDB:2DDM}.
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


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