PDXY_YERPE
ID PDXY_YERPE Reviewed; 286 AA.
AC Q7CIR8; Q74TK1;
DT 09-JAN-2007, integrated into UniProtKB/Swiss-Prot.
DT 05-JUL-2004, sequence version 1.
DT 03-AUG-2022, entry version 102.
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};
GN OrderedLocusNames=YPO2368, y1967, YP_2154;
OS Yersinia pestis.
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Yersiniaceae; Yersinia.
OX NCBI_TaxID=632;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=KIM10+ / Biovar Mediaevalis;
RX PubMed=12142430; DOI=10.1128/jb.184.16.4601-4611.2002;
RA Deng W., Burland V., Plunkett G. III, Boutin A., Mayhew G.F., Liss P.,
RA Perna N.T., Rose D.J., Mau B., Zhou S., Schwartz D.C., Fetherston J.D.,
RA Lindler L.E., Brubaker R.R., Plano G.V., Straley S.C., McDonough K.A.,
RA Nilles M.L., Matson J.S., Blattner F.R., Perry R.D.;
RT "Genome sequence of Yersinia pestis KIM.";
RL J. Bacteriol. 184:4601-4611(2002).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=CO-92 / Biovar Orientalis;
RX PubMed=11586360; DOI=10.1038/35097083;
RA Parkhill J., Wren B.W., Thomson N.R., Titball R.W., Holden M.T.G.,
RA Prentice M.B., Sebaihia M., James K.D., Churcher C.M., Mungall K.L.,
RA Baker S., Basham D., Bentley S.D., Brooks K., Cerdeno-Tarraga A.-M.,
RA Chillingworth T., Cronin A., Davies R.M., Davis P., Dougan G., Feltwell T.,
RA Hamlin N., Holroyd S., Jagels K., Karlyshev A.V., Leather S., Moule S.,
RA Oyston P.C.F., Quail M.A., Rutherford K.M., Simmonds M., Skelton J.,
RA Stevens K., Whitehead S., Barrell B.G.;
RT "Genome sequence of Yersinia pestis, the causative agent of plague.";
RL Nature 413:523-527(2001).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=91001 / Biovar Mediaevalis;
RX PubMed=15368893; DOI=10.1093/dnares/11.3.179;
RA Song Y., Tong Z., Wang J., Wang L., Guo Z., Han Y., Zhang J., Pei D.,
RA Zhou D., Qin H., Pang X., Han Y., Zhai J., Li M., Cui B., Qi Z., Jin L.,
RA Dai R., Chen F., Li S., Ye C., Du Z., Lin W., Wang J., Yu J., Yang H.,
RA Wang J., Huang P., Yang R.;
RT "Complete genome sequence of Yersinia pestis strain 91001, an isolate
RT avirulent to humans.";
RL DNA Res. 11:179-197(2004).
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; AE009952; AAM85533.1; -; Genomic_DNA.
DR EMBL; AL590842; CAL20996.1; -; Genomic_DNA.
DR EMBL; AE017042; AAS62362.1; -; Genomic_DNA.
DR PIR; AI0288; AI0288.
DR RefSeq; WP_002210961.1; NZ_WUCM01000049.1.
DR RefSeq; YP_002347334.1; NC_003143.1.
DR PDB; 3PZS; X-ray; 1.89 A; A/B=1-286.
DR PDBsum; 3PZS; -.
DR AlphaFoldDB; Q7CIR8; -.
DR SMR; Q7CIR8; -.
DR STRING; 214092.YPO2368; -.
DR PaxDb; Q7CIR8; -.
DR DNASU; 1146914; -.
DR EnsemblBacteria; AAM85533; AAM85533; y1967.
DR EnsemblBacteria; AAS62362; AAS62362; YP_2154.
DR GeneID; 57976307; -.
DR KEGG; ype:YPO2368; -.
DR KEGG; ypk:y1967; -.
DR KEGG; ypm:YP_2154; -.
DR PATRIC; fig|214092.21.peg.2775; -.
DR eggNOG; COG2240; Bacteria.
DR HOGENOM; CLU_046496_3_0_6; -.
DR OMA; CPNQLEL; -.
DR UniPathway; UPA01068; UER00298.
DR Proteomes; UP000000815; Chromosome.
DR Proteomes; UP000001019; Chromosome.
DR Proteomes; UP000002490; Chromosome.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
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; IBA:GO_Central.
DR GO; GO:0016310; P:phosphorylation; IEA:UniProtKB-KW.
DR GO; GO:0009443; P:pyridoxal 5'-phosphate salvage; IBA:GO_Central.
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..286
FT /note="Pyridoxal kinase PdxY"
FT /id="PRO_0000269838"
FT BINDING 9
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01639"
FT BINDING 44..45
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01639"
FT BINDING 111
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 208..211
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01639"
FT BINDING 223
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01639"
FT STRAND 3..14
FT /evidence="ECO:0007829|PDB:3PZS"
FT HELIX 18..27
FT /evidence="ECO:0007829|PDB:3PZS"
FT STRAND 31..42
FT /evidence="ECO:0007829|PDB:3PZS"
FT HELIX 44..46
FT /evidence="ECO:0007829|PDB:3PZS"
FT STRAND 51..53
FT /evidence="ECO:0007829|PDB:3PZS"
FT HELIX 56..68
FT /evidence="ECO:0007829|PDB:3PZS"
FT HELIX 72..74
FT /evidence="ECO:0007829|PDB:3PZS"
FT STRAND 77..80
FT /evidence="ECO:0007829|PDB:3PZS"
FT HELIX 86..102
FT /evidence="ECO:0007829|PDB:3PZS"
FT STRAND 107..110
FT /evidence="ECO:0007829|PDB:3PZS"
FT TURN 117..119
FT /evidence="ECO:0007829|PDB:3PZS"
FT HELIX 125..133
FT /evidence="ECO:0007829|PDB:3PZS"
FT HELIX 135..138
FT /evidence="ECO:0007829|PDB:3PZS"
FT STRAND 140..142
FT /evidence="ECO:0007829|PDB:3PZS"
FT HELIX 146..153
FT /evidence="ECO:0007829|PDB:3PZS"
FT HELIX 160..171
FT /evidence="ECO:0007829|PDB:3PZS"
FT STRAND 176..180
FT /evidence="ECO:0007829|PDB:3PZS"
FT HELIX 184..186
FT /evidence="ECO:0007829|PDB:3PZS"
FT STRAND 192..198
FT /evidence="ECO:0007829|PDB:3PZS"
FT STRAND 203..209
FT /evidence="ECO:0007829|PDB:3PZS"
FT HELIX 221..234
FT /evidence="ECO:0007829|PDB:3PZS"
FT HELIX 239..259
FT /evidence="ECO:0007829|PDB:3PZS"
FT TURN 267..270
FT /evidence="ECO:0007829|PDB:3PZS"
FT HELIX 271..275
FT /evidence="ECO:0007829|PDB:3PZS"
SQ SEQUENCE 286 AA; 31185 MW; AE864688A8180040 CRC64;
MKNILSIQSH VVFGHAGNSA AEFPMRRMGV NVWPLNTVQF SNHTQYGHWT GCVMPASHLT
DIVQGIADID RLKDCDAVLS GYIGSPEQGS HILAAVAQVK QANPDAWYFC DPVMGHPEKG
CIVAPGVAEF FCNEALPASD MIAPNLLELE QLSGERVENV EQAVQVARSL CARGPKVVLV
KHLSRAGYHA DCFEMLLVTA DDAWHICRPL VDFGKRQPVG VGDLTSGLLL VNLLKGEPLD
KALEHVTAAV YEVMLKTQEM GEYELQVVAA QETIVTPICQ FTAVRL
