PDXY_ECOLI
ID PDXY_ECOLI Reviewed; 287 AA.
AC P77150;
DT 01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT 15-JAN-2008, sequence version 3.
DT 03-AUG-2022, entry version 162.
DE RecName: Full=Pyridoxal kinase PdxY {ECO:0000303|PubMed:9537380};
DE Short=PL kinase {ECO:0000303|PubMed:9537380};
DE EC=2.7.1.35 {ECO:0000269|PubMed:15249053, ECO:0000269|PubMed:9537380};
DE AltName: Full=Pyridoxal kinase 2 {ECO:0000303|PubMed:15249053};
DE Short=PL kinase 2 {ECO:0000303|PubMed:15249053};
GN Name=pdxY {ECO:0000303|PubMed:9537380}; Synonyms=ydgS;
GN OrderedLocusNames=b1636, JW1628;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=9097039; DOI=10.1093/dnares/3.6.363;
RA Aiba H., Baba T., Fujita K., Hayashi K., Inada T., Isono K., Itoh T.,
RA Kasai H., Kashimoto K., Kimura S., Kitakawa M., Kitagawa M., Makino K.,
RA Miki T., Mizobuchi K., Mori H., Mori T., Motomura K., Nakade S.,
RA Nakamura Y., Nashimoto H., Nishio Y., Oshima T., Saito N., Sampei G.,
RA Seki Y., Sivasundaram S., Tagami H., Takeda J., Takemoto K., Takeuchi Y.,
RA Wada C., Yamamoto Y., Horiuchi T.;
RT "A 570-kb DNA sequence of the Escherichia coli K-12 genome corresponding to
RT the 28.0-40.1 min region on the linkage map.";
RL DNA Res. 3:363-377(1996).
RN [2]
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 [3]
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 [4]
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 [5]
RP FUNCTION, AND CATALYTIC ACTIVITY.
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 [6]
RP X-RAY CRYSTALLOGRAPHY (2.22 ANGSTROMS) IN COMPLEX WITH PYRIDOXAL, AND
RP SUBUNIT.
RX PubMed=15547280; DOI=10.1128/jb.186.23.8074-8082.2004;
RA Safo M.K., Musayev F.N., Hunt S., di Salvo M.L., Scarsdale N., Schirch V.;
RT "Crystal structure of the PdxY protein from Escherichia coli.";
RL J. Bacteriol. 186:8074-8082(2004).
RN [7]
RP X-RAY CRYSTALLOGRAPHY (1.96 ANGSTROMS) OF 2-287.
RX PubMed=16021622; DOI=10.1002/prot.20541;
RA Badger J., Sauder J.M., Adams J.M., Antonysamy S., Bain K., Bergseid M.G.,
RA Buchanan S.G., Buchanan M.D., Batiyenko Y., Christopher J.A., Emtage S.,
RA Eroshkina A., Feil I., Furlong E.B., Gajiwala K.S., Gao X., He D.,
RA Hendle J., Huber A., Hoda K., Kearins P., Kissinger C., Laubert B.,
RA Lewis H.A., Lin J., Loomis K., Lorimer D., Louie G., Maletic M.,
RA Marsh C.D., Miller I., Molinari J., Muller-Dieckmann H.J., Newman J.M.,
RA Noland B.W., Pagarigan B., Park F., Peat T.S., Post K.W., Radojicic S.,
RA Ramos A., Romero R., Rutter M.E., Sanderson W.E., Schwinn K.D., Tresser J.,
RA Winhoven J., Wright T.A., Wu L., Xu J., Harris T.J.R.;
RT "Structural analysis of a set of proteins resulting from a bacterial
RT genomics project.";
RL Proteins 60:787-796(2005).
CC -!- FUNCTION: Pyridoxal kinase involved in the salvage pathway of pyridoxal
CC 5'-phosphate (PLP). Catalyzes the phosphorylation of pyridoxal to PLP
CC in vivo, but shows very low activity compared to PdxK. Displays a low
CC level of pyridoxine kinase activity when overexpressed, which is
CC however not physiologically relevant. {ECO:0000269|PubMed:15249053,
CC 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 -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01639};
CC -!- PATHWAY: Cofactor metabolism; pyridoxal 5'-phosphate salvage; pyridoxal
CC 5'-phosphate from pyridoxal: step 1/1. {ECO:0000269|PubMed:9537380}.
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:15547280}.
CC -!- DISRUPTION PHENOTYPE: Cells lacking this gene and cells lacking both
CC pdxY and pdxK are not auxotrophs, meaning that the de novo pathway of
CC PLP biosynthesis is functional. For PLP salvage, the pdxY single mutant
CC can use both pyridoxine and pyridoxal, the pdxK single mutant can use
CC pyridoxal but not pyridoxine, and the double mutant can no longer use
CC both compounds. {ECO:0000269|PubMed:9537380}.
CC -!- SIMILARITY: Belongs to the pyridoxine kinase family. PdxY subfamily.
CC {ECO:0000305}.
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DR EMBL; U00096; AAC74708.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA15397.1; -; Genomic_DNA.
DR PIR; F64920; F64920.
DR RefSeq; NP_416153.1; NC_000913.3.
DR RefSeq; WP_001307229.1; NZ_SSTT01000001.1.
DR PDB; 1TD2; X-ray; 2.22 A; A/B=1-287.
DR PDB; 1VI9; X-ray; 1.96 A; A/B/C/D=2-287.
DR PDBsum; 1TD2; -.
DR PDBsum; 1VI9; -.
DR AlphaFoldDB; P77150; -.
DR SMR; P77150; -.
DR BioGRID; 4263486; 7.
DR IntAct; P77150; 2.
DR STRING; 511145.b1636; -.
DR DrugBank; DB02153; 3-sulfino-L-alanine.
DR jPOST; P77150; -.
DR PaxDb; P77150; -.
DR PRIDE; P77150; -.
DR EnsemblBacteria; AAC74708; AAC74708; b1636.
DR EnsemblBacteria; BAA15397; BAA15397; BAA15397.
DR GeneID; 66674472; -.
DR GeneID; 946162; -.
DR KEGG; ecj:JW1628; -.
DR KEGG; eco:b1636; -.
DR PATRIC; fig|511145.12.peg.1707; -.
DR EchoBASE; EB3699; -.
DR eggNOG; COG2240; Bacteria.
DR HOGENOM; CLU_046496_3_0_6; -.
DR InParanoid; P77150; -.
DR OMA; CPNQLEL; -.
DR PhylomeDB; P77150; -.
DR BioCyc; EcoCyc:PDXY-MON; -.
DR BioCyc; MetaCyc:PDXY-MON; -.
DR BRENDA; 2.7.1.35; 2026.
DR UniPathway; UPA01068; UER00298.
DR EvolutionaryTrace; P77150; -.
DR PRO; PR:P77150; -.
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:0042802; F:identical protein binding; IDA:EcoCyc.
DR GO; GO:0000287; F:magnesium ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0008478; F:pyridoxal kinase activity; IDA:EcoCyc.
DR GO; GO:0016310; P:phosphorylation; IEA:UniProtKB-KW.
DR GO; GO:0009443; P:pyridoxal 5'-phosphate salvage; IMP:EcoliWiki.
DR GO; GO:0042817; P:pyridoxal metabolic process; IMP:EcoliWiki.
DR GO; GO:0042819; P:vitamin B6 biosynthetic process; IMP:EcoliWiki.
DR CDD; cd01173; pyridoxal_pyridoxamine_kinase; 1.
DR Gene3D; 3.40.1190.20; -; 1.
DR HAMAP; MF_01639; PdxY; 1.
DR InterPro; IPR013749; PM/HMP-P_kinase-1.
DR InterPro; IPR004625; PyrdxlKinase.
DR InterPro; IPR023685; Pyridoxal_kinase_PdxY.
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; Nucleotide-binding;
KW Reference proteome; Transferase.
FT CHAIN 1..287
FT /note="Pyridoxal kinase PdxY"
FT /id="PRO_0000213345"
FT BINDING 10
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:15547280"
FT BINDING 45..46
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:15547280"
FT BINDING 112
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:P40191"
FT BINDING 144
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:P40191"
FT BINDING 149
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:P40191"
FT BINDING 182
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:P40191"
FT BINDING 209..212
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:P40191"
FT BINDING 224
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:15547280"
FT STRAND 4..9
FT /evidence="ECO:0007829|PDB:1VI9"
FT STRAND 12..15
FT /evidence="ECO:0007829|PDB:1VI9"
FT HELIX 19..28
FT /evidence="ECO:0007829|PDB:1VI9"
FT STRAND 32..43
FT /evidence="ECO:0007829|PDB:1VI9"
FT HELIX 45..47
FT /evidence="ECO:0007829|PDB:1VI9"
FT STRAND 52..54
FT /evidence="ECO:0007829|PDB:1VI9"
FT HELIX 57..69
FT /evidence="ECO:0007829|PDB:1VI9"
FT HELIX 73..75
FT /evidence="ECO:0007829|PDB:1VI9"
FT STRAND 78..81
FT /evidence="ECO:0007829|PDB:1VI9"
FT HELIX 87..103
FT /evidence="ECO:0007829|PDB:1VI9"
FT STRAND 108..111
FT /evidence="ECO:0007829|PDB:1VI9"
FT TURN 118..120
FT /evidence="ECO:0007829|PDB:1VI9"
FT HELIX 128..134
FT /evidence="ECO:0007829|PDB:1VI9"
FT HELIX 136..139
FT /evidence="ECO:0007829|PDB:1VI9"
FT STRAND 141..143
FT /evidence="ECO:0007829|PDB:1VI9"
FT HELIX 147..154
FT /evidence="ECO:0007829|PDB:1VI9"
FT HELIX 161..173
FT /evidence="ECO:0007829|PDB:1VI9"
FT STRAND 177..181
FT /evidence="ECO:0007829|PDB:1VI9"
FT HELIX 185..187
FT /evidence="ECO:0007829|PDB:1VI9"
FT STRAND 188..190
FT /evidence="ECO:0007829|PDB:1VI9"
FT STRAND 193..199
FT /evidence="ECO:0007829|PDB:1VI9"
FT STRAND 204..210
FT /evidence="ECO:0007829|PDB:1VI9"
FT HELIX 222..235
FT /evidence="ECO:0007829|PDB:1VI9"
FT HELIX 240..260
FT /evidence="ECO:0007829|PDB:1VI9"
FT TURN 268..272
FT /evidence="ECO:0007829|PDB:1VI9"
FT HELIX 273..276
FT /evidence="ECO:0007829|PDB:1VI9"
SQ SEQUENCE 287 AA; 31322 MW; CD131649887E559A CRC64;
MMKNILAIQS HVVYGHAGNS AAEFPMRRLG ANVWPLNTVQ FSNHTQYGKW TGCVMPPSHL
TEIVQGIAAI DKLHTCDAVL SGYLGSAEQG EHILGIVRQV KAANPQAKYF CDPVMGHPEK
GCIVAPGVAE FHVRHGLPAS DIIAPNLVEL EILCEHAVNN VEEAVLAARE LIAQGPQIVL
VKHLARAGYS RDRFEMLLVT ADEAWHISRP LVDFGMRQPV GVGDVTSGLL LVKLLQGATL
QEALEHVTAA VYEIMVTTKA MQEYELQVVA AQDRIAKPEH YFSATKL
