PDXK_BACSU
ID PDXK_BACSU Reviewed; 271 AA.
AC P39610;
DT 01-FEB-1995, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-1995, sequence version 1.
DT 03-AUG-2022, entry version 135.
DE RecName: Full=Pyridoxine kinase;
DE EC=2.7.1.35;
DE AltName: Full=PN/PL/PM kinase;
DE AltName: Full=Pyridoxal kinase;
DE AltName: Full=Pyridoxamine kinase;
DE AltName: Full=Vitamin B6 kinase;
GN Name=pdxK; Synonyms=ywdB; OrderedLocusNames=BSU38020; ORFNames=ipa-52r;
OS Bacillus subtilis (strain 168).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus.
OX NCBI_TaxID=224308;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=168;
RX PubMed=7934828; DOI=10.1111/j.1365-2958.1993.tb01963.x;
RA Glaser P., Kunst F., Arnaud M., Coudart M.P., Gonzales W., Hullo M.-F.,
RA Ionescu M., Lubochinsky B., Marcelino L., Moszer I., Presecan E.,
RA Santana M., Schneider E., Schweizer J., Vertes A., Rapoport G., Danchin A.;
RT "Bacillus subtilis genome project: cloning and sequencing of the 97 kb
RT region from 325 degrees to 333 degrees.";
RL Mol. Microbiol. 10:371-384(1993).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=168;
RX PubMed=9384377; DOI=10.1038/36786;
RA Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V.,
RA Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R.,
RA Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S.,
RA Bruschi C.V., Caldwell B., Capuano V., Carter N.M., Choi S.-K.,
RA Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F.,
RA Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D.,
RA Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M.,
RA Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P.,
RA Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K.,
RA Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S.,
RA Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y.,
RA Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G.,
RA Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J.,
RA Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C.,
RA Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S.,
RA Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B.,
RA Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S.,
RA Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M.,
RA Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y.,
RA Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J.,
RA Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A.,
RA Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M.,
RA Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S.,
RA Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E.,
RA Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K.,
RA Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E.,
RA Yoshikawa H., Danchin A.;
RT "The complete genome sequence of the Gram-positive bacterium Bacillus
RT subtilis.";
RL Nature 390:249-256(1997).
RN [3]
RP FUNCTION AS PYRIDOXAL KINASE, CATALYTIC ACTIVITY, AND BIOPHYSICOCHEMICAL
RP PROPERTIES.
RC STRAIN=168 / CU1065;
RX PubMed=14973012; DOI=10.1128/jb.186.5.1571-1573.2004;
RA Park J.-H., Burns K., Kinsland C., Begley T.P.;
RT "Characterization of two kinases involved in thiamine pyrophosphate and
RT pyridoxal phosphate biosynthesis in Bacillus subtilis: 4-amino-5-
RT hydroxymethyl-2-methylpyrimidine kinase and pyridoxal kinase.";
RL J. Bacteriol. 186:1571-1573(2004).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) IN COMPLEX WITH ADP, AND SUBUNIT.
RX PubMed=16978644; DOI=10.1016/j.jmb.2006.08.013;
RA Newman J.A., Das S.K., Sedelnikova S.E., Rice D.W.;
RT "The crystal structure of an ADP complex of Bacillus subtilis pyridoxal
RT kinase provides evidence for the parallel emergence of enzyme activity
RT during evolution.";
RL J. Mol. Biol. 363:520-530(2006).
CC -!- FUNCTION: Phosphorylates B6 vitamers; functions in a salvage pathway.
CC Uses pyridoxal, pyridoxine, and pyridoxamine as substrates. Can also
CC use hydroxymethylpyrimidine (HMP) as substrate.
CC {ECO:0000269|PubMed:14973012}.
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:14973012};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=2 mM for HMP {ECO:0000269|PubMed:14973012};
CC KM=46.6 uM for pyridoxal {ECO:0000269|PubMed:14973012};
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:16978644}.
CC -!- SIMILARITY: Belongs to the ThiD family. {ECO:0000305}.
CC -!- CAUTION: Was originally annotated in the complete genome as thiD.
CC {ECO:0000305|PubMed:9384377}.
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DR EMBL; X73124; CAA51608.1; -; Genomic_DNA.
DR EMBL; AL009126; CAB15828.1; -; Genomic_DNA.
DR PIR; S39707; S39707.
DR RefSeq; NP_391681.1; NC_000964.3.
DR RefSeq; WP_003242645.1; NZ_JNCM01000034.1.
DR PDB; 2I5B; X-ray; 2.80 A; A/B/C/D/E=1-271.
DR PDBsum; 2I5B; -.
DR AlphaFoldDB; P39610; -.
DR SMR; P39610; -.
DR STRING; 224308.BSU38020; -.
DR PaxDb; P39610; -.
DR PRIDE; P39610; -.
DR EnsemblBacteria; CAB15828; CAB15828; BSU_38020.
DR GeneID; 937262; -.
DR KEGG; bsu:BSU38020; -.
DR PATRIC; fig|224308.179.peg.4116; -.
DR eggNOG; COG0351; Bacteria.
DR InParanoid; P39610; -.
DR OMA; KDEVGYA; -.
DR PhylomeDB; P39610; -.
DR BioCyc; BSUB:BSU38020-MON; -.
DR SABIO-RK; P39610; -.
DR EvolutionaryTrace; P39610; -.
DR Proteomes; UP000001570; Chromosome.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0008902; F:hydroxymethylpyrimidine kinase activity; IBA:GO_Central.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0008972; F:phosphomethylpyrimidine kinase activity; IBA:GO_Central.
DR GO; GO:0008478; F:pyridoxal kinase activity; IEA:UniProtKB-EC.
DR GO; GO:0016310; P:phosphorylation; IEA:UniProtKB-KW.
DR GO; GO:0009228; P:thiamine biosynthetic process; IBA:GO_Central.
DR CDD; cd01169; HMPP_kinase; 1.
DR Gene3D; 3.40.1190.20; -; 1.
DR InterPro; IPR045029; HMP/HMP-P_kinase.
DR InterPro; IPR004399; HMP/HMP-P_kinase_dom.
DR InterPro; IPR013749; PM/HMP-P_kinase-1.
DR InterPro; IPR029056; Ribokinase-like.
DR PANTHER; PTHR20858; PTHR20858; 1.
DR Pfam; PF08543; Phos_pyr_kin; 1.
DR SUPFAM; SSF53613; SSF53613; 1.
DR TIGRFAMs; TIGR00097; HMP-P_kinase; 1.
PE 1: Evidence at protein level;
KW 3D-structure; ATP-binding; Kinase; Magnesium; Metal-binding;
KW Nucleotide-binding; Reference proteome; Transferase.
FT CHAIN 1..271
FT /note="Pyridoxine kinase"
FT /id="PRO_0000192017"
FT BINDING 141
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT BINDING 144
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 178..182
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT BINDING 190
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT BINDING 206
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT BINDING 215
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT BINDING 240
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT STRAND 5..13
FT /evidence="ECO:0007829|PDB:2I5B"
FT STRAND 16..18
FT /evidence="ECO:0007829|PDB:2I5B"
FT HELIX 19..29
FT /evidence="ECO:0007829|PDB:2I5B"
FT STRAND 33..44
FT /evidence="ECO:0007829|PDB:2I5B"
FT TURN 46..50
FT /evidence="ECO:0007829|PDB:2I5B"
FT STRAND 52..56
FT /evidence="ECO:0007829|PDB:2I5B"
FT HELIX 59..72
FT /evidence="ECO:0007829|PDB:2I5B"
FT STRAND 76..80
FT /evidence="ECO:0007829|PDB:2I5B"
FT HELIX 86..98
FT /evidence="ECO:0007829|PDB:2I5B"
FT STRAND 102..106
FT /evidence="ECO:0007829|PDB:2I5B"
FT STRAND 111..113
FT /evidence="ECO:0007829|PDB:2I5B"
FT STRAND 115..120
FT /evidence="ECO:0007829|PDB:2I5B"
FT HELIX 121..130
FT /evidence="ECO:0007829|PDB:2I5B"
FT HELIX 132..134
FT /evidence="ECO:0007829|PDB:2I5B"
FT STRAND 136..138
FT /evidence="ECO:0007829|PDB:2I5B"
FT HELIX 142..149
FT /evidence="ECO:0007829|PDB:2I5B"
FT HELIX 157..168
FT /evidence="ECO:0007829|PDB:2I5B"
FT TURN 169..171
FT /evidence="ECO:0007829|PDB:2I5B"
FT STRAND 173..178
FT /evidence="ECO:0007829|PDB:2I5B"
FT HELIX 180..182
FT /evidence="ECO:0007829|PDB:2I5B"
FT STRAND 185..193
FT /evidence="ECO:0007829|PDB:2I5B"
FT STRAND 198..203
FT /evidence="ECO:0007829|PDB:2I5B"
FT HELIX 214..227
FT /evidence="ECO:0007829|PDB:2I5B"
FT HELIX 232..248
FT /evidence="ECO:0007829|PDB:2I5B"
FT STRAND 253..256
FT /evidence="ECO:0007829|PDB:2I5B"
FT HELIX 264..268
FT /evidence="ECO:0007829|PDB:2I5B"
SQ SEQUENCE 271 AA; 29017 MW; CCC0DA345DA3724F CRC64;
MSMHKALTIA GSDSSGGAGI QADLKTFQEK NVYGMTALTV IVAMDPNNSW NHQVFPIDTD
TIRAQLATIT DGIGVDAMKT GMLPTVDIIE LAAKTIKEKQ LKNVVIDPVM VCKGANEVLY
PEHAQALREQ LAPLATVITP NLFEASQLSG MDELKTVDDM IEAAKKIHAL GAQYVVITGG
GKLKHEKAVD VLYDGETAEV LESEMIDTPY THGAGCTFSA AVTAELAKGA EVKEAIYAAK
EFITAAIKES FPLNQYVGPT KHSALRLNQQ S
