PDXK_BOMMO
ID PDXK_BOMMO Reviewed; 298 AA.
AC Q1PCB1;
DT 10-FEB-2021, integrated into UniProtKB/Swiss-Prot.
DT 16-MAY-2006, sequence version 1.
DT 03-AUG-2022, entry version 87.
DE RecName: Full=Pyridoxal kinase {ECO:0000303|PubMed:17707212, ECO:0000303|PubMed:22079857, ECO:0000303|PubMed:26780217, ECO:0000303|PubMed:27106120, ECO:0000303|Ref.3};
DE Short=PLK {ECO:0000303|PubMed:17707212, ECO:0000303|PubMed:22079857, ECO:0000303|PubMed:27106120, ECO:0000303|Ref.3};
DE EC=2.7.1.35 {ECO:0000269|PubMed:17707212, ECO:0000269|PubMed:22079857, ECO:0000269|Ref.3};
DE AltName: Full=BmPLK {ECO:0000303|PubMed:22079857, ECO:0000303|PubMed:27106120};
DE AltName: Full=PL kinase {ECO:0000303|PubMed:26780217};
DE AltName: Full=Pyridoxine kinase {ECO:0000305};
GN Name=Pdxk {ECO:0000312|EMBL:ABE28378.1};
OS Bombyx mori (Silk moth).
OC Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota;
OC Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Bombycoidea;
OC Bombycidae; Bombycinae; Bombyx.
OX NCBI_TaxID=7091 {ECO:0000312|EMBL:ABE28378.1};
RN [1] {ECO:0000312|EMBL:ABE28378.1}
RP NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, AND CATALYTIC ACTIVITY.
RC TISSUE=Larval fat body {ECO:0000303|PubMed:17707212};
RX PubMed=17707212; DOI=10.1016/s1673-8527(07)60077-0;
RA Shi R., Zhang J., Jiang C., Huang L.;
RT "Bombyx mori pyridoxal kinase cDNA cloning and enzymatic
RT characterization.";
RL J. Genet. Genomics 34:683-690(2007).
RN [2] {ECO:0000312|EnsemblMetazoa:BGIBMGA005472-TA}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=p50T {ECO:0000312|EnsemblMetazoa:BGIBMGA005472-TA};
RX PubMed=19121390; DOI=10.1016/j.ibmb.2008.11.004;
RG International Silkworm Genome Consortium;
RT "The genome of a lepidopteran model insect, the silkworm Bombyx mori.";
RL Insect Biochem. Mol. Biol. 38:1036-1045(2008).
RN [3]
RP FUNCTION, CATALYTIC ACTIVITY, COFACTOR, ACTIVITY REGULATION,
RP BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT, REACTION MECHANISM, 3D-STRUCTURE
RP MODELING, AND CIRCULAR DICHROISM ANALYSIS.
RX DOI=10.14411/eje.2011.003;
RA Huang S.-H., Ma W., Zhang P.-P., Zhang J.-Y., Xie Y.-F., Huang L.-Q.;
RT "Recombinant expression, purification and characterization of Bombyx mori
RT (Lepidoptera: Bombycidae) pyridoxal kinase.";
RL Eur. J. Entomol. 108:25-34(2011).
RN [4]
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, MUTAGENESIS OF
RP THR-47; ILE-54; ARG-88; ASN-121 AND TRP-230, AND CIRCULAR DICHROISM
RP ANALYSIS.
RX PubMed=22079857; DOI=10.1016/j.cbpb.2011.10.009;
RA Huang S., Shu T., Zhang J., Ma W., Wei S., Huang L.;
RT "Functional significance of some particular amino acid residues in Bombyx
RT mori pyridoxal kinase.";
RL Comp. Biochem. Physiol. 161:155-160(2012).
RN [5]
RP TISSUE SPECIFICITY, DEVELOPMENTAL STAGE, AND INDUCTION.
RX PubMed=26780217; DOI=10.1016/j.cbpb.2016.01.002;
RA Huang S., Yang H., Yao L., Zhang J., Huang L.;
RT "Effect of exogenous hormones on transcription levels of pyridoxal 5'-
RT phosphate biosynthetic enzymes in the silkworm (Bombyx mori).";
RL Comp. Biochem. Physiol. 194:20-24(2016).
RN [6]
RP DEVELOPMENTAL STAGE, AND DISRUPTION PHENOTYPE.
RX PubMed=27106120; DOI=10.1016/j.gene.2016.04.035;
RA Huang S., Yao L., Zhang J., Huang L.;
RT "Direct and indirect effects of RNA interference against pyridoxal kinase
RT and pyridoxine 5'-phosphate oxidase genes in Bombyx mori.";
RL Gene 587:48-52(2016).
CC -!- FUNCTION: Catalyzes the phosphorylation of the dietary vitamin B6
CC vitamers pyridoxal (PL), pyridoxine (PN) and pyridoxamine (PM) to form
CC pyridoxal 5'-phosphate (PLP), pyridoxine 5'-phosphate (PNP) and
CC pyridoxamine 5'-phosphate (PMP), respectively (PubMed:17707212, Ref.3,
CC PubMed:22079857) (By similarity). PLP is the active form of vitamin B6,
CC and acts as a cofactor for over 140 different enzymatic reactions
CC (Probable). {ECO:0000250|UniProtKB:O00764, ECO:0000269|PubMed:17707212,
CC ECO:0000269|PubMed:22079857, ECO:0000269|Ref.3, ECO:0000305}.
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:17707212,
CC ECO:0000269|PubMed:22079857, ECO:0000269|Ref.3};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:10225;
CC Evidence={ECO:0000269|PubMed:17707212, ECO:0000269|PubMed:22079857,
CC ECO:0000269|Ref.3};
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:0000250|UniProtKB:O00764};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:25105;
CC Evidence={ECO:0000250|UniProtKB:O00764};
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:0000250|UniProtKB:O00764};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:25109;
CC Evidence={ECO:0000250|UniProtKB:O00764};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000269|Ref.3};
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105; Evidence={ECO:0000269|Ref.3};
CC Note=Divalent metal cations. Zn(2+) is the most effective cation for
CC catalysis. {ECO:0000269|Ref.3};
CC -!- ACTIVITY REGULATION: Activity is stimulated by Mg(2+). Activated by
CC K(+) in the presence of triethanolamine (pH 7.3). {ECO:0000269|Ref.3}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=57.9 uM for ATP (in the presence of 0.5 mM ZnCl(2), at pH 5.5 and
CC 37 degrees Celsius) {ECO:0000269|Ref.3};
CC KM=44.1 uM for pyridoxal (PL) (in the presence of 0.5 mM ZnCl(2), at
CC pH 5.5 and 37 degrees Celsius) {ECO:0000269|Ref.3};
CC KM=65.0 uM for ATP (in the presence of 0.5 mM ZnCl(2), at pH 5.5 and
CC 37 degrees Celsius) {ECO:0000269|PubMed:22079857};
CC KM=55.4 uM for pyridoxal (PL) (in the presence of 0.5 mM ZnCl(2), at
CC pH 5.5 and 37 degrees Celsius) {ECO:0000269|PubMed:22079857};
CC Vmax=2.23 umol/min/mg enzyme toward ATP (in the presence of 0.5 mM
CC ZnCl(2), at pH 5.5 and 37 degrees Celsius) {ECO:0000269|Ref.3};
CC Vmax=2.45 umol/min/mg enzyme toward pyridoxal (PL) (in the presence
CC of 0.5 mM ZnCl(2), at pH 5.5 and 37 degrees Celsius)
CC {ECO:0000269|Ref.3};
CC Note=kcat is 1.23 sec(-1) for ATP. kcat is 1.35 sec(-1) for PL.
CC {ECO:0000269|Ref.3};
CC pH dependence:
CC Optimum pH is 5.5-6.0. Activity decreases slowly above pH 6.0, to
CC approximately 35% of the maximum at pH 8.5. Inactive below pH 4.5.
CC {ECO:0000269|Ref.3};
CC Temperature dependence:
CC Optimum temperature is 50 degrees Celsius. Stable below 40 degrees
CC Celsius. {ECO:0000269|Ref.3};
CC -!- PATHWAY: Cofactor metabolism; pyridoxal 5'-phosphate salvage; pyridoxal
CC 5'-phosphate from pyridoxal: step 1/1. {ECO:0000250|UniProtKB:O00764}.
CC -!- PATHWAY: Cofactor metabolism; pyridoxal 5'-phosphate salvage;
CC pyridoxamine 5'-phosphate from pyridoxamine: step 1/1.
CC {ECO:0000250|UniProtKB:O00764}.
CC -!- PATHWAY: Cofactor metabolism; pyridoxal 5'-phosphate salvage;
CC pyridoxine 5'-phosphate from pyridoxine: step 1/1.
CC {ECO:0000250|UniProtKB:O00764}.
CC -!- SUBUNIT: Homodimer. {ECO:0000269|Ref.3}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm, cytosol
CC {ECO:0000250|UniProtKB:O00764}.
CC -!- TISSUE SPECIFICITY: Expressed in silk gland and fat body of the larva.
CC {ECO:0000269|PubMed:26780217}.
CC -!- DEVELOPMENTAL STAGE: Expressed in fifth instar larva (PubMed:26780217,
CC PubMed:27106120). In the silk gland, highest level on the first day of
CC 5th instar larva, then displaying a decreasing trend daily. In the fat
CC body, expression level is high in the early and late stages, and low in
CC the middle stage of 5th instar larva (PubMed:26780217).
CC {ECO:0000269|PubMed:26780217, ECO:0000269|PubMed:27106120}.
CC -!- INDUCTION: Expression is up-regulated by exogenous molting hormone
CC (beta-ecdysterone) and down-regulated by exogenous juvenile hormone
CC (JH) III in the silk gland and fat body of the fifth instar larva.
CC {ECO:0000269|PubMed:26780217}.
CC -!- DISRUPTION PHENOTYPE: RNAi-mediated knockdown of this protein causes
CC significant decrease in transcription levels of pyridoxal 5'-phosphate
CC (PLP)-dependent enzymes phosphoserine aminotransferase (PSAT) and
CC aspartate aminotransferase (glutamic-oxaloacetic transaminase) in silk
CC gland, fat body and midgut of the fifth instar larva.
CC {ECO:0000269|PubMed:27106120}.
CC -!- SIMILARITY: Belongs to the pyridoxine kinase family. {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; DQ452397; ABE28378.1; -; mRNA.
DR EMBL; BABH01013892; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; BABH01013893; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR RefSeq; NP_001037440.1; NM_001043975.1.
DR AlphaFoldDB; Q1PCB1; -.
DR SMR; Q1PCB1; -.
DR STRING; 7091.BGIBMGA005472-TA; -.
DR EnsemblMetazoa; BGIBMGA005472-RA; BGIBMGA005472-TA; BGIBMGA005472.
DR GeneID; 693009; -.
DR KEGG; bmor:693009; -.
DR CTD; 8566; -.
DR eggNOG; KOG2599; Eukaryota.
DR HOGENOM; CLU_046496_1_1_1; -.
DR InParanoid; Q1PCB1; -.
DR OMA; CPNQLEL; -.
DR OrthoDB; 1091630at2759; -.
DR BRENDA; 2.7.1.35; 890.
DR UniPathway; UPA01068; UER00298.
DR UniPathway; UPA01068; UER00299.
DR UniPathway; UPA01068; UER00300.
DR Proteomes; UP000005204; Unassembled WGS sequence.
DR GO; GO:0005829; C:cytosol; IEA:UniProtKB-SubCell.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0008478; F:pyridoxal kinase activity; IEA:UniProtKB-EC.
DR GO; GO:0016310; P:phosphorylation; IEA:UniProtKB-KW.
DR GO; GO:0009443; P:pyridoxal 5'-phosphate salvage; IEA:InterPro.
DR CDD; cd01173; pyridoxal_pyridoxamine_kinase; 1.
DR Gene3D; 3.40.1190.20; -; 1.
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 ATP-binding; Cytoplasm; Kinase; Magnesium; Metal-binding;
KW Nucleotide-binding; Reference proteome; Sodium; Transferase.
FT CHAIN 1..298
FT /note="Pyridoxal kinase"
FT /id="PRO_0000451920"
FT ACT_SITE 221
FT /note="Proton acceptor"
FT /evidence="ECO:0000250|UniProtKB:O00764"
FT BINDING 14
FT /ligand="pyridoxal"
FT /ligand_id="ChEBI:CHEBI:17310"
FT /evidence="ECO:0000250|UniProtKB:O00764"
FT BINDING 47
FT /ligand="pyridoxal"
FT /ligand_id="ChEBI:CHEBI:17310"
FT /evidence="ECO:0000250|UniProtKB:O00764"
FT BINDING 47
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000250|UniProtKB:O00764"
FT BINDING 115
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:O00764"
FT BINDING 115
FT /ligand="Na(+)"
FT /ligand_id="ChEBI:CHEBI:29101"
FT /evidence="ECO:0000250|UniProtKB:O00764"
FT BINDING 120
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250|UniProtKB:O00764"
FT BINDING 125
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000250|UniProtKB:P82197"
FT BINDING 146
FT /ligand="Na(+)"
FT /ligand_id="ChEBI:CHEBI:29101"
FT /evidence="ECO:0000250|UniProtKB:O00764"
FT BINDING 148..151
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:O00764"
FT BINDING 184..185
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:O00764"
FT BINDING 212..214
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:O00764"
FT BINDING 219
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:O00764"
FT BINDING 220..221
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000250|UniProtKB:O00764"
FT MUTAGEN 47
FT /note="T->N: 60% decrease in specific activity and about 2-
FT fold reduction in affinity for pyridoxal (PL) substrate and
FT ATP compared to wild-type."
FT /evidence="ECO:0000269|PubMed:22079857"
FT MUTAGEN 54
FT /note="I->F: 46% decrease in specific activity and about 2-
FT fold reduction in affinity for pyridoxal (PL) substrate and
FT ATP compared to wild-type."
FT /evidence="ECO:0000269|PubMed:22079857"
FT MUTAGEN 88
FT /note="R->I: 62% decrease in specific activity and about 2-
FT fold reduction in affinity for pyridoxal (PL) substrate and
FT ATP compared to wild-type."
FT /evidence="ECO:0000269|PubMed:22079857"
FT MUTAGEN 121
FT /note="N->E: No effect in catalytic activity."
FT /evidence="ECO:0000269|PubMed:22079857"
FT MUTAGEN 230
FT /note="W->E: Loss of catalytic activity. Misfolding of the
FT protein."
FT /evidence="ECO:0000269|PubMed:22079857"
SQ SEQUENCE 298 AA; 33097 MW; 22BC11E02C741369 CRC64;
MSQDDTPRVL SIQSHVVHGY VGNKSAVFPL QVLGFEVDSI NTVQFSTHTA YKHIKGYVLN
NDQMKELVEG LVLNEVDYYT HFLTGYSRSP DSLREIAKII KQLREKNPNL IYVCDPVMGD
NGKMYVPEEI LPVYRDVLVP LADILTPNQF EAELITGIPM KDLDGALRVI QRLHDMGVKT
VVLSSTDLGD EENMIGLAST GGSCYKIPIP KVEATFTGTG DLFAALFLAW SHLTGNDVKL
ALEKTIATLQ SIVVDTYQTA RASHLTGKIP PRFTELRLVQ NKTVIEDPKI KLKAVKIN
