DB code: S00904

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 S00678 S00705 S00903 S00905 S00453 D00416

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
P77150 Pyridoxamine kinase
PM kinase
EC 2.7.1.35
NP_416153.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_489900.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
PF08543 (Phos_pyr_kin)
[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
P77150 PDXY_ECOLI ATP + pyridoxal = ADP + pyridoxal 5'-phosphate. Homodimer.

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

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00305 C00238 C00002 C00250 C00008 C00018
E.C.
Compound Magnesium Potassium ATP pyridoxal ADP pyridoxal 5'-phosphate
Type divalent metal (Ca2+, Mg2+) 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
 		29103
 29103
 		15422
 15422
 		17310
 17310
 		16761
 16761
 		18405
 18405
PubChem 888
 888
 		813
 813
 		5957
 5957
 		1050
 1050
 		6022
 6022
 		1051
 1051
1td2A00 Unbound Unbound Unbound Bound:PXL Unbound Unbound
1td2B00 Unbound Unbound Analogue:SO4 Bound:PXL Unbound Unbound
1vi9A00 Unbound Unbound Analogue:SO4 Unbound Unbound Unbound
1vi9B00 Unbound Unbound Analogue:SO4 Unbound Unbound Unbound
1vi9C00 Unbound Unbound Analogue:SO4 Unbound Unbound Unbound
1vi9D00 Unbound Unbound Analogue:SO4 Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
literature [4], [5], [6], [9], [12]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1td2A00 ASP 224 ASP 112;GLU 149(Potassium binding) GLY 221;VAL 222;GLY 223
1td2B00 ASP 224 ASP 112;GLU 149(Potassium binding) GLY 221;VAL 222;GLY 223
1vi9A00 ASP 224 ASP 112;GLU 149(Potassium binding) GLY 221;VAL 222;GLY 223
1vi9B00 ASP 224 ASP 112;GLU 149(Potassium binding) GLY 221;VAL 222;GLY 223
1vi9C00 ASP 224 ASP 112;GLU 149(Potassium binding) GLY 221;VAL 222;GLY 223
1vi9D00 ASP 224 ASP 112;GLU 149(Potassium binding) GLY 221;VAL 222;GLY 223

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[4]
Fig.5, p.46387-46389
[5]
p.8079
[6]
p.17462, p.17464-17465
[9]
p.1305
[12]
Scheme 1, p.14

References
[1]
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
[2]
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
[3]
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
[4]
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
[5]
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
[6]
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
[7]
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
[8]
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
[9]
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
[10]
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
[11]
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
[12]
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
This enzyme belongs to the ribokinase superfamily.
According to the literature [9] and [12], this enzyme is a member of K+-activaated Type-I Enzymes. By comparison with its homologous enzymes, the binding site for potassium ion has been annotated for this enzyme. Moreover, although this enzyme uses magnesium ion as a cofactor, its binding site has not been elucidated yet. The potassium ion may stabilize the negative charge on the gamma-phosphate group of ATP, whereas the magnesium ion may stabilize the negative charge on beta- and gamma-phosphate groups (see [8] and [11]).
Although this enzyme seems to be homologous to the counterpart enzyme from mammals (see S00678), the magnesium binding site is not conserved in this enzyme.

Created Updated
2009-08-24 2012-01-10