PDXY_PARXL
ID PDXY_PARXL Reviewed; 288 AA.
AC Q141E8;
DT 09-JAN-2007, integrated into UniProtKB/Swiss-Prot.
DT 22-AUG-2006, sequence version 1.
DT 03-AUG-2022, entry version 89.
DE RecName: Full=Pyridoxal kinase PdxY {ECO:0000255|HAMAP-Rule:MF_01639};
DE Short=PL kinase {ECO:0000255|HAMAP-Rule:MF_01639};
DE EC=2.7.1.35 {ECO:0000255|HAMAP-Rule:MF_01639};
GN Name=pdxY {ECO:0000255|HAMAP-Rule:MF_01639}; OrderedLocusNames=Bxeno_A1503;
GN ORFNames=Bxe_A2936;
OS Paraburkholderia xenovorans (strain LB400).
OC Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales;
OC Burkholderiaceae; Paraburkholderia.
OX NCBI_TaxID=266265;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=LB400;
RX PubMed=17030797; DOI=10.1073/pnas.0606924103;
RA Chain P.S.G., Denef V.J., Konstantinidis K.T., Vergez L.M., Agullo L.,
RA Reyes V.L., Hauser L., Cordova M., Gomez L., Gonzalez M., Land M., Lao V.,
RA Larimer F., LiPuma J.J., Mahenthiralingam E., Malfatti S.A., Marx C.J.,
RA Parnell J.J., Ramette A., Richardson P., Seeger M., Smith D., Spilker T.,
RA Sul W.J., Tsoi T.V., Ulrich L.E., Zhulin I.B., Tiedje J.M.;
RT "Burkholderia xenovorans LB400 harbors a multi-replicon, 9.73-Mbp genome
RT shaped for versatility.";
RL Proc. Natl. Acad. Sci. U.S.A. 103:15280-15287(2006).
CC -!- FUNCTION: Pyridoxal kinase involved in the salvage pathway of pyridoxal
CC 5'-phosphate (PLP). Catalyzes the phosphorylation of pyridoxal to PLP.
CC {ECO:0000255|HAMAP-Rule:MF_01639}.
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:0000255|HAMAP-Rule:MF_01639};
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:0000255|HAMAP-
CC Rule:MF_01639}.
CC -!- SUBUNIT: Homodimer. {ECO:0000255|HAMAP-Rule:MF_01639}.
CC -!- SIMILARITY: Belongs to the pyridoxine kinase family. PdxY subfamily.
CC {ECO:0000255|HAMAP-Rule:MF_01639}.
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DR EMBL; CP000270; ABE30041.1; -; Genomic_DNA.
DR RefSeq; WP_011487752.1; NZ_CP008760.1.
DR PDB; 5TRW; X-ray; 1.60 A; A=1-288.
DR PDBsum; 5TRW; -.
DR AlphaFoldDB; Q141E8; -.
DR SMR; Q141E8; -.
DR STRING; 266265.Bxe_A2936; -.
DR EnsemblBacteria; ABE30041; ABE30041; Bxe_A2936.
DR KEGG; bxb:DR64_617; -.
DR KEGG; bxe:Bxe_A2936; -.
DR PATRIC; fig|266265.5.peg.1551; -.
DR eggNOG; COG2240; Bacteria.
DR OMA; CPNQLEL; -.
DR OrthoDB; 1480223at2; -.
DR UniPathway; UPA01068; UER00298.
DR Proteomes; UP000001817; Chromosome 1.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR GO; GO:0000287; F:magnesium ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0008478; F:pyridoxal kinase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0016310; P:phosphorylation; IEA:UniProtKB-KW.
DR GO; GO:0009443; P:pyridoxal 5'-phosphate salvage; IEA:UniProtKB-UniRule.
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..288
FT /note="Pyridoxal kinase PdxY"
FT /id="PRO_0000269802"
FT BINDING 10
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01639"
FT BINDING 45..46
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01639"
FT BINDING 112
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01639"
FT BINDING 143
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01639"
FT BINDING 148
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01639"
FT BINDING 181
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01639"
FT BINDING 222
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01639"
FT STRAND 4..15
FT /evidence="ECO:0007829|PDB:5TRW"
FT HELIX 19..29
FT /evidence="ECO:0007829|PDB:5TRW"
FT STRAND 32..43
FT /evidence="ECO:0007829|PDB:5TRW"
FT HELIX 45..47
FT /evidence="ECO:0007829|PDB:5TRW"
FT STRAND 52..54
FT /evidence="ECO:0007829|PDB:5TRW"
FT HELIX 57..69
FT /evidence="ECO:0007829|PDB:5TRW"
FT HELIX 73..75
FT /evidence="ECO:0007829|PDB:5TRW"
FT STRAND 78..81
FT /evidence="ECO:0007829|PDB:5TRW"
FT HELIX 87..103
FT /evidence="ECO:0007829|PDB:5TRW"
FT STRAND 108..111
FT /evidence="ECO:0007829|PDB:5TRW"
FT HELIX 127..133
FT /evidence="ECO:0007829|PDB:5TRW"
FT HELIX 135..137
FT /evidence="ECO:0007829|PDB:5TRW"
FT STRAND 140..142
FT /evidence="ECO:0007829|PDB:5TRW"
FT HELIX 146..153
FT /evidence="ECO:0007829|PDB:5TRW"
FT HELIX 160..171
FT /evidence="ECO:0007829|PDB:5TRW"
FT STRAND 176..183
FT /evidence="ECO:0007829|PDB:5TRW"
FT STRAND 192..201
FT /evidence="ECO:0007829|PDB:5TRW"
FT STRAND 203..209
FT /evidence="ECO:0007829|PDB:5TRW"
FT HELIX 220..233
FT /evidence="ECO:0007829|PDB:5TRW"
FT HELIX 238..258
FT /evidence="ECO:0007829|PDB:5TRW"
FT TURN 266..269
FT /evidence="ECO:0007829|PDB:5TRW"
FT HELIX 270..274
FT /evidence="ECO:0007829|PDB:5TRW"
SQ SEQUENCE 288 AA; 31403 MW; 5720289FC3A534F5 CRC64;
MTKNVLSIQS HVVFGHAGNS AAVFPMRRLG VNVWPLNTVQ FSNHTQYGHW TGGAIDATQM
VELVDGIGAI GMLPRCDAVL SGYLGTPEQA QSVLEIVKAV KAANPRAWYF CDPVMGAVSG
CKVEPGIQEF LVRTMPGVAD AMAPNHTELQ RLVGREIETL EEAVTACREL IARGPKLVLV
KHLLDRNSPA DRFNMLVVTE REAWMGQRPL YPFARQPVGV GDLTSAVFVA RTLLGDSIRA
AFEHTLAAVN AVVKATWQAG RYELELVAAQ SEIAQPREWF DAWVGDTA
