DB code: S00903

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 S00904 S00905 S00453 D00416

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
P40191 Pyridoxine kinase
EC 2.7.1.35
Pyridoxal kinase
Vitamin B6 kinase
Pyridoxamine kinase
PN/PL/PM kinase
NP_416913.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_490654.1 (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
P40191 PDXK_ECOLI ATP + pyridoxal = ADP + pyridoxal 5'-phosphate. Zinc or magnesium.

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
29105
29103
15422
17310
16761
18405
PubChem 888
32051
813
5957
1050
6022
1051
2ddmA00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound
2ddmB00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound
2ddoA00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_MG Unbound Unbound Bound:ATP Unbound Unbound Unbound
2ddoB00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound
2ddwA00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Bound:PXL Unbound Unbound
2ddwB00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Bound:PXL Unbound Unbound

Reference for Active-site residues
resource references E.C.
literature [4], [6], [8], [9], [12]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
2ddmA00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 233 TYR 136;GLU 162(Magnesium binding) GLY 230;THR 231;GLY 232
2ddmB00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 233 TYR 136;GLU 162(Magnesium binding) GLY 230;THR 231;GLY 232
2ddoA00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 233 TYR 136;GLU 162(Magnesium binding) GLY 230;THR 231;GLY 232
2ddoB00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 233 TYR 136;GLU 162(Magnesium binding) GLY 230;THR 231;GLY 232
2ddwA00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 233 TYR 136;GLU 162(Magnesium binding) GLY 230;THR 231;GLY 232
2ddwB00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 233 TYR 136;GLU 162(Magnesium binding) GLY 230;THR 231;GLY 232

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[4]
Fig.5, p.46387-46389
[6]
p.17462, p.17464-17465
[8]
p.4545, p.4547
[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 ribokinase superfamily (see [10]).
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 [8]).
This enzyme belongs to Prokaryote pdxK group, whereas the counterpart enzymes from prokaryote can be classified into two groups, Eukaryote pdxK group (S00678 in EzCatDB) and Prokaryote pdxY group (S00904 in EzCatDB) (see [10]).
This enzyme belongs to the K+ activated type I enzymes (see [8] & [10]). However, the binding site for the potassium ion has not been elucidated yet.
Although the reaction mechanism can be similar to the homologous enzyme from Eukarote (S00678 in EzCatDB), the detailed mechanism has not been clear.

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