DB code: S00678

RLCP classification 3.103.70035.456 : Transfer
CATH domain 3.40.1190.20 : UDP-N-acetylmuramoyl-L-alanine Catalytic domain
E.C. 2.7.1.35
CSA
M-CSA
MACiE

CATH domain Related DB codes (homologues)
3.40.1190.20 : UDP-N-acetylmuramoyl-L-alanine S00534 S00541 S00705 S00903 S00904 S00905 S00453 D00416

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
P82197 Pyridoxal kinase
EC 2.7.1.35
Pyridoxine kinase
NP_001009220.1 (Protein)
NM_001009220.1 (DNA/RNA sequence)
PF00294 (PfkB)
[Graphical View]
O00764 Pyridoxal kinase
EC 2.7.1.35
Pyridoxine kinase
NP_003672.1 (Protein)
NM_003681.4 (DNA/RNA sequence)
PF00294 (PfkB)
[Graphical View]

KEGG enzyme name
Pyridoxal kinase
Pyridoxal kinase (phosphorylating)
Pyridoxal 5-phosphate-kinase
Pyridoxal phosphokinase
Pyridoxine kinase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P82197 PDXK_SHEEP ATP + pyridoxal = ADP + pyridoxal 5'-phosphate. Homodimer. Cytoplasm. Divalent cations. Zn(2+) is more efficient than Mg(2+).
O00764 PDXK_HUMAN ATP + pyridoxal = ADP + pyridoxal 5'-phosphate. Homodimer (Probable). Cytoplasm. Divalent cations. Zn(2+) is more efficient than Mg(2+).

KEGG Pathways
Map code Pathways E.C.
MAP00750 Vitamin B6 metabolism

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00305 C00038 C00238 C00002 C00250 C00008 C00018
E.C.
Compound Magnesium Zinc Potassium ATP pyridoxal ADP pyridoxal 5'-phosphate
Type divalent metal (Ca2+, Mg2+) heavy metal univalent metal (Na+, K+) amine group,nucleotide aromatic ring (with nitrogen atoms),carbohydrate amine group,nucleotide aromatic ring (with nitrogen atoms),phosphate group/phosphate ion
ChEBI 18420
 18420
 		29105
 29105
 		29103
 29103
 		15422
 15422
 		17310
 17310
 		16761
 16761
 		18405
 18405
PubChem 888
 888
 		32051
 32051
 		813
 813
 		5957
 5957
 		1050
 1050
 		6022
 6022
 		1051
 1051
1lhpA00 Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1lhpB00 Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1lhrA00 Unbound Bound:_ZN Bound:__K Bound:ATP Unbound Unbound Unbound
1lhrB00 Unbound Bound:_ZN Bound:__K Bound:ATP Unbound Unbound Unbound
1rftA00 Unbound Bound:_ZN Bound:__K Analogue:ACP Analogue:PXM Unbound Unbound
1rfuA00 Unbound Bound:_ZN Unbound Unbound Unbound Bound:ADP Bound:PLP
1rfuB00 Unbound Bound:_ZN Unbound Unbound Unbound Bound:ADP Bound:PLP
1rfuC00 Unbound Bound:_ZN Unbound Unbound Unbound Bound:ADP Bound:PLP
1rfuD00 Unbound Bound:_ZN Unbound Unbound Unbound Bound:ADP Bound:PLP
1rfuE00 Unbound Bound:_ZN Unbound Unbound Unbound Bound:ADP Bound:PLP
1rfuF00 Unbound Bound:_ZN Unbound Unbound Unbound Bound:ADP Bound:PLP
1rfuG00 Unbound Bound:_ZN Unbound Unbound Unbound Bound:ADP Bound:PLP
1rfuH00 Unbound Bound:_ZN Unbound Unbound Unbound Bound:ADP Bound:PLP
1rfvA00 Unbound Bound:_ZN Unbound Unbound Unbound Bound:ADP Unbound
1rfvB00 Unbound Bound:_ZN Unbound Unbound Unbound Bound:ADP Unbound
1ygjA00 Unbound Unbound Unbound Unbound Analogue:RMC Unbound Unbound
1ygkA00 Unbound Unbound Unbound Unbound Analogue:RRC Unbound Unbound
1yhjA00 Unbound Unbound Unbound Unbound Analogue:R6C Unbound Unbound
2ajpA00 Bound:_MG Unbound Unbound Analogue:ANP Unbound Unbound Unbound
2ajpB00 Bound:_MG Unbound Unbound Analogue:ANP Unbound Unbound Unbound
2f7kA00 Unbound Unbound Unbound Unbound Unbound Unbound Unbound
2f7kB00 Unbound Unbound Unbound Unbound Unbound Unbound Unbound
2yxtA00 Unbound Unbound Analogue:_NA Unbound Unbound Unbound Unbound
2yxtB00 Unbound Unbound Analogue:_NA Unbound Unbound Unbound Unbound
2yxuA00 Bound:_MG Unbound Analogue:_NA Bound:ATP Unbound Unbound Unbound
2yxuB00 Bound:_MG Unbound Analogue:_NA Bound:ATP Unbound Unbound Unbound
3fhxA00 Bound:_MG Unbound Analogue:_NA Bound:ATP Bound:PXL Unbound Unbound
3fhxB00 Bound:_MG Unbound Analogue:_NA Bound:ATP Bound:PXL Unbound Bound:PLP
3fhyA00 Bound:_MG Unbound Analogue:_NA Bound:ATP Unbound Unbound Unbound
3fhyB00 Bound:_MG Unbound Analogue:_NA Bound:ATP Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
literature [6], [8], [11], [14], [15]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1lhpA00 ASP 235 ASP 113;GLU 153(pottasium binding);ASP 118(magnesium binding);THR 148;THR 186(monovalent cation binding) GLY 232;THR 233;GLY 234;ASP 235
1lhpB00 ASP 235 ASP 113;GLU 153(pottasium binding);ASP 118(magnesium binding);THR 148;THR 186(monovalent cation binding) GLY 232;THR 233;GLY 234;ASP 235
1lhrA00 ASP 235 ASP 113;GLU 153(pottasium binding);ASP 118(magnesium binding);THR 148;THR 186(monovalent cation binding) GLY 232;THR 233;GLY 234;ASP 235
1lhrB00 ASP 235 ASP 113;GLU 153(pottasium binding);ASP 118(magnesium binding);THR 148;THR 186(monovalent cation binding) GLY 232;THR 233;GLY 234;ASP 235
1rftA00 ASP 235 ASP 113;GLU 153(pottasium binding);ASP 118(magnesium binding);THR 148;THR 186(monovalent cation binding) GLY 232;THR 233;GLY 234;ASP 235
1rfuA00 ASP 235 ASP 113;GLU 153(pottasium binding);ASP 118(magnesium binding);THR 148;THR 186(monovalent cation binding) GLY 232;THR 233;GLY 234;ASP 235
1rfuB00 ASP 235 ASP 113;GLU 153(pottasium binding);ASP 118(magnesium binding);THR 148;THR 186(monovalent cation binding) GLY 232;THR 233;GLY 234;ASP 235
1rfuC00 ASP 235 ASP 113;GLU 153(pottasium binding);ASP 118(magnesium binding);THR 148;THR 186(monovalent cation binding) GLY 232;THR 233;GLY 234;ASP 235
1rfuD00 ASP 235 ASP 113;GLU 153(pottasium binding);ASP 118(magnesium binding);THR 148;THR 186(monovalent cation binding) GLY 232;THR 233;GLY 234;ASP 235
1rfuE00 ASP 235 ASP 113;GLU 153(pottasium binding);ASP 118(magnesium binding);THR 148;THR 186(monovalent cation binding) GLY 232;THR 233;GLY 234;ASP 235
1rfuF00 ASP 235 ASP 113;GLU 153(pottasium binding);ASP 118(magnesium binding);THR 148;THR 186(monovalent cation binding) GLY 232;THR 233;GLY 234;ASP 235
1rfuG00 ASP 235 ASP 113;GLU 153(pottasium binding);ASP 118(magnesium binding);THR 148;THR 186(monovalent cation binding) GLY 232;THR 233;GLY 234;ASP 235
1rfuH00 ASP 235 ASP 113;GLU 153(pottasium binding);ASP 118(magnesium binding);THR 148;THR 186(monovalent cation binding) GLY 232;THR 233;GLY 234;ASP 235
1rfvA00 ASP 235 ASP 113;GLU 153(pottasium binding);ASP 118(magnesium binding);THR 148;THR 186(monovalent cation binding) GLY 232;THR 233;GLY 234;ASP 235
1rfvB00 ASP 235 ASP 113;GLU 153(pottasium binding);ASP 118(magnesium binding);THR 148;THR 186(monovalent cation binding) GLY 232;THR 233;GLY 234;ASP 235
1ygjA00 ASP 235 ASP 113;GLU 153(pottasium binding);ASP 118(magnesium binding);THR 148;THR 186(monovalent cation binding) GLY 232;THR 233;GLY 234;ASP 235
1ygkA00 ASP 235 ASP 113;GLU 153(pottasium binding);ASP 118(magnesium binding);THR 148;THR 186(monovalent cation binding) GLY 232;THR 233;GLY 234;ASP 235
1yhjA00 ASP 235 ASP 113;GLU 153(pottasium binding);ASP 118(magnesium binding);THR 148;THR 186(monovalent cation binding) GLY 232;THR 233;GLY 234;ASP 235
2ajpA00 ASP 235 ASP 113;GLU 153(pottasium binding);ASP 118(magnesium binding);THR 148;THR 186(monovalent cation binding) GLY 232;THR 233;GLY 234;ASP 235
2ajpB00 ASP 235 ASP 113;GLU 153(pottasium binding);ASP 118(magnesium binding);THR 148;THR 186(monovalent cation binding) GLY 232;THR 233;GLY 234;ASP 235
2f7kA00 ASP 235 ASP 113;GLU 153(pottasium binding);ASP 118(magnesium binding);THR 148;THR 186(monovalent cation binding) GLY 232;THR 233;GLY 234;ASP 235
2f7kB00 ASP 235 ASP 113;GLU 153(pottasium binding);ASP 118(magnesium binding);THR 148;THR 186(monovalent cation binding) GLY 232;THR 233;GLY 234;ASP 235
2yxtA00 ASP 235 ASP 113;GLU 153(pottasium binding);ASP 118(magnesium binding);THR 148;THR 186(monovalent cation binding) GLY 232;THR 233;GLY 234;ASP 235
2yxtB00 ASP 235 ASP 113;GLU 153(pottasium binding);ASP 118(magnesium binding);THR 148;THR 186(monovalent cation binding) GLY 232;THR 233;GLY 234;ASP 235
2yxuA00 ASP 235 ASP 113;GLU 153(pottasium binding);ASP 118(magnesium binding);THR 148;THR 186(monovalent cation binding) GLY 232;THR 233;GLY 234;ASP 235
2yxuB00 ASP 235 ASP 113;GLU 153(pottasium binding);ASP 118(magnesium binding);THR 148;THR 186(monovalent cation binding) GLY 232;THR 233;GLY 234;ASP 235
3fhxA00 ASP 113;GLU 153(pottasium binding);ASP 118(magnesium binding);THR 148;THR 186(monovalent cation binding) GLY 232;THR 233;GLY 234; mutant D235A
3fhxB00 ASP 113;GLU 153(pottasium binding);ASP 118(magnesium binding);THR 148;THR 186(monovalent cation binding) GLY 232;THR 233;GLY 234; mutant D235A
3fhyA00 ASP 113;GLU 153(pottasium binding);ASP 118(magnesium binding);THR 148;THR 186(monovalent cation binding) GLY 232;THR 233;GLY 234; mutant D235N
3fhyB00 ASP 113;GLU 153(pottasium binding);ASP 118(magnesium binding);THR 148;THR 186(monovalent cation binding) GLY 232;THR 233;GLY 234; mutant D235N

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[6]
Fig.5, p.46387-46389
[8]
p.17462, p.17464-17465
[11]
p.1305
[14]
p.2191
[15]
Scheme 1, p.14

References
[1]
Resource
Comments
Medline ID
PubMed ID 16590515
Journal Proc Natl Acad Sci U S A
Year 1959
Volume 45
Pages 1371-9
Authors McCormick DB, Snell EE
Title PYRIDOXAL KINASE OF HUMAN BRAIN AND ITS INHIBITION BY HYDRAZINE DERIVATIVES.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 6288708
Journal J Biol Chem
Year 1982
Volume 257
Pages 12136-40
Authors Churchich JE, Wu C
Title Nucleoside phosphorothioates as probes of the nucleotide binding site of brain pyridoxal kinase.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 9252787
Journal Enzyme Protein
Year 1996
Volume 49
Pages 291-304
Authors Laine-Cessac P, Allain P
Title Kinetic studies of the effects of K+, Na+ and Li+ on the catalytic activity of human erythrocyte pyridoxal kinase.
Related PDB
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 9843365
Journal Biochemistry
Year 1998
Volume 37
Pages 15607-20
Authors Mathews II, Erion MD, Ealick SE
Title Structure of human adenosine kinase at 1.5 A resolution.
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 9519409
Journal Structure
Year 1998
Volume 6
Pages 183-93
Authors Sigrell JA, Cameron AD, Jones TA, Mowbray SL
Title Structure of Escherichia coli ribokinase in complex with ribose and dinucleotide determined to 1.8 A resolution: insights into a new family of kinase structures.
Related PDB
Related UniProtKB
[6]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) IN COMPLEX WITH SUBSTRATE; ADP AND COFACTOR.
Medline ID
PubMed ID 12235162
Journal J Biol Chem
Year 2002
Volume 277
Pages 46385-90
Authors Li MH, Kwok F, Chang WR, Lau CK, Zhang JP, Lo SC, Jiang T, Liang DC
Title Crystal structure of brain pyridoxal kinase, a novel member of the ribokinase superfamily.
Related PDB 1lhp 1lhr
Related UniProtKB P82197
[7]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.22 ANGSTROMS) OF 2-287, SUBUNIT.
Medline ID
PubMed ID 15547280
Journal J Bacteriol
Year 2004
Volume 186
Pages 8074-82
Authors Safo MK, Musayev FN, Hunt S, di Salvo ML, Scarsdale N, Schirch V
Title Crystal structure of the PdxY Protein from Escherichia coli.
Related PDB 1td2
Related UniProtKB P77150
[8]
Resource
Comments
Medline ID
PubMed ID 14722069
Journal J Biol Chem
Year 2004
Volume 279
Pages 17459-65
Authors Li MH, Kwok F, Chang WR, Liu SQ, Lo SC, Zhang JP, Jiang T, Liang DC
Title Conformational changes in the reaction of pyridoxal kinase.
Related PDB 1rft 1rfu 1rfv
Related UniProtKB
[9]
Resource
Comments
Medline ID
PubMed ID 15985434
Journal J Biol Chem
Year 2005
Volume 280
Pages 31220-9
Authors Tang L, Li MH, Cao P, Wang F, Chang WR, Bach S, Reinhardt J, Ferandin Y, Galons H, Wan Y, Gray N, Meijer L, Jiang T, Liang DC
Title Crystal structure of pyridoxal kinase in complex with roscovitine and derivatives.
Related PDB 1ygk 1ygj 1yhj
Related UniProtKB
[10]
Resource
Comments
Medline ID
PubMed ID 16740960
Journal J Bacteriol
Year 2006
Volume 188
Pages 4542-52
Authors Safo MK, Musayev FN, di Salvo ML, Hunt S, Claude JB, Schirch V
Title Crystal structure of pyridoxal kinase from the Escherichia coli pdxK gene: implications for the classification of pyridoxal kinases.
Related PDB 2ddm 2ddo 2ddw
Related UniProtKB
[11]
Resource
Comments
Medline ID
PubMed ID 16267046
Journal J Biol Chem
Year 2006
Volume 281
Pages 1305-8
Authors Di Cera E
Title A structural perspective on enzymes activated by monovalent cations.
Related PDB
Related UniProtKB
[12]
Resource
Comments
Medline ID
PubMed ID 16600635
Journal J Struct Biol
Year 2006
Volume 154
Pages 327-32
Authors Cao P, Gong Y, Tang L, Leung YC, Jiang T
Title Crystal structure of human pyridoxal kinase.
Related PDB 2f7k
Related UniProtKB
[13]
Resource
Comments
Medline ID
PubMed ID 17015484
Journal Physiol Rev
Year 2006
Volume 86
Pages 1049-92
Authors Page MJ, Di Cera E
Title Role of Na+ and K+ in enzyme function.
Related PDB
Related UniProtKB
[14]
Resource
Comments
Medline ID
PubMed ID 17766369
Journal Protein Sci
Year 2007
Volume 16
Pages 2184-94
Authors Musayev FN, di Salvo ML, Ko TP, Gandhi AK, Goswami A, Schirch V, Safo MK
Title Crystal Structure of human pyridoxal kinase: structural basis of M(+) and M(2+) activation.
Related PDB 2yxt 2yxu
Related UniProtKB
[15]
Resource
Comments
Medline ID
PubMed ID 19351586
Journal Biochem Biophys Res Commun
Year 2009
Volume 381
Pages 12-5
Authors Gandhi AK, Ghatge MS, Musayev FN, Sease A, Aboagye SO, di Salvo ML, Schirch V, Safo MK
Title Kinetic and structural studies of the role of the active site residue Asp235 of human pyridoxal kinase.
Related PDB 3fhx 3fhy
Related UniProtKB

Comments
For this enzyme, zinc ion is more efficiant cofactor than magnesium ion. Whereas zinc ion is bound to beta- and gamma-phosphate groups of ATP, magnesium ion is bound to alpha- and beta-phosphate groups as well as Asp118. Thus, these divalent metal ions interacts with the enzyme and substrate differently from each other.
Meanwhile, potassium and sodium ions are bound to more similar position. However, whereas potassium ion is bound to Asp113, Glu153, Thr148 and Thr186 as well as beta-phosphate of ATP, sodium ion is bound to Thr148 and Thr186 as well as ATP gamma-phosphate.
According to the literature [8] and [14], the reaction preceeds as follows:
(0) Zinc ion stabilizes the negatively-charged transferred group (gamma-phosphate) and leaving group (beta-phosphate) of ATP, whereas potassium ion, bound to sidechains of Asp113, Glu153 and Thr186, and mainchain carbonyl oxygen of Thr148, may stabilize the leaving group, beta-phosphate of ATP.
(1) Asp235 acts as a general base to deprotonate 5'-hydroxyl group of pyridoxal, to activate it.
(2) The activated 5'-oxygen atom makes a nucleophilic attack on the gamma-phosphate of ATP, leading to the transition state. The transferred gamma-phosphate in the transition-state must be stabilized by an anion hole composed of mainchain amide groups of Gly232-Thr233-Gly234-Asp235, along with magnesium ion. The leaving group can be stabilized by the same magnesium ion and the potassium ion. Here, the reaction proceeds throuhg SN2-like mechanism.
This enzyme belongs to ribokinase superfamily (see [12] and [13]).
This enzyme, pyridoxal kinase (EC 2.7.1.35), can be classified into three groups, based on the sequence and the metal binding sites (see [10]).
This enzyme belongs to Eukaryote pdxK group, whereas the counterpart enzymes from prokaryote can be classified into two groups, Prokaryote pdxK group (S00903 in EzCatDB) and Prokaryote pdxY group (S00904 in EzCatDB) (see [10]).
This enzyme belongs to the K+ activated type I enzymes (see [11] & [13]).
(3) Finally, the transferrd gamma-phosphate is bonded to the 5'-oxygen of pyridoxal, to complete the raction.

Created Updated
2009-08-24 2012-01-12