DB code: S00905

RLCP classification 3.103.78020.387 : 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 S00678 S00705 S00903 S00904 S00453 D00416

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
P39610 Phosphomethylpyrimidine kinase
EC 2.7.4.7
HMP-phosphate kinase
HMP-P kinase
HMPP kinase
NP_391681.1 (Protein)
NC_000964.3 (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
P39610 PDXK_BACSU 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 C00002 C00250 C00008 C00018
E.C.
Compound Magnesium ATP Pyridoxal ADP Pyridoxal phosphate
Type divalent metal (Ca2+, Mg2+) amine group,nucleotide aromatic ring (with nitrogen atoms),carbohydrate amine group,nucleotide aromatic ring (with nitrogen atoms),phosphate group/phosphate ion
ChEBI 18420
15422
17310
16761
18405
PubChem 888
5957
1050
6022
1051
2i5bA00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Bound:ADP Unbound
2i5bB00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Bound:ADP Unbound
2i5bC00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Bound:ADP Unbound
2i5bD00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Bound:ADP Unbound
2i5bE00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Bound:ADP Unbound

Reference for Active-site residues
resource references E.C.
literature [6], [7]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
2i5bA00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 182;CYS 216 ASP 107;GLU 144;THR 139(Magnesium binding) GLY 213;ALA 214;GLY 215;CYS 216
2i5bB00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 182;CYS 216 ASP 107;GLU 144;THR 139(Magnesium binding) GLY 213;ALA 214;GLY 215;CYS 216
2i5bC00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 182;CYS 216 ASP 107;GLU 144;THR 139(Magnesium binding) GLY 213;ALA 214;GLY 215;CYS 216
2i5bD00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 182;CYS 216 ASP 107;GLU 144;THR 139(Magnesium binding) GLY 213;ALA 214;GLY 215;CYS 216
2i5bE00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 182;CYS 216 ASP 107;GLU 144;THR 139(Magnesium binding) GLY 213;ALA 214;GLY 215;CYS 216

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[6]
Fig.6, p1815-1816
[7]
Fig.2, p.525

References
[1]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.84 ANGSTROMS).
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 1rkd
Related UniProtKB P0A9J6
[2]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.5 ANGSTROMS) IN COMPLEX WITH SUBSTRATE, HOMOTRIMERIZATION, AND MUTAGENESIS OF CYS-198.
Medline ID
PubMed ID 10891066
Journal Biochemistry
Year 2000
Volume 39
Pages 7868-77
Authors Campobasso N, Mathews II, Begley TP, Ealick SE
Title Crystal structure of 4-methyl-5-beta-hydroxyethylthiazole kinase from Bacillus subtilis at 1.5 A resolution.
Related PDB 1c3q 1esq 1esj 1ekq 1ekk
Related UniProtKB P39593
[3]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF 23-266.
Medline ID
PubMed ID 11839308
Journal Structure
Year 2002
Volume 10
Pages 225-35
Authors Cheng G, Bennett EM, Begley TP, Ealick SE
Title Crystal structure of 4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate kinase from Salmonella typhimurium at 2.3 A resolution.
Related PDB 1jxh 1jxi
Related UniProtKB P55882
[4]
Resource
Comments
Medline ID
PubMed ID 14675553
Journal Curr Opin Struct Biol
Year 2003
Volume 13
Pages 739-47
Authors Settembre E, Begley TP, Ealick SE
Title Structural biology of enzymes of the thiamin biosynthesis pathway.
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID
Journal Int J Mol Sci
Year 2004
Volume 5
Pages 141-153
Authors Edyta Dyguda, Borys Szefczyk and W. A. Sokalski
Title The Mechanism of Phosphoryl Transfer Reaction and the Role of Active Site Residues on the Basis of Ribokinase-Like Kinases
Related PDB
Related UniProtKB
[6]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS).
Medline ID
PubMed ID 15458630
Journal Structure
Year 2004
Volume 12
Pages 1809-21
Authors Zhang Y, Dougherty M, Downs DM, Ealick SE
Title Crystal structure of an aminoimidazole riboside kinase from Salmonella enterica: implications for the evolution of the ribokinase superfamily.
Related PDB 1tyy 1tz3 1tz6
Related UniProtKB Q8ZKR2
[7]
Resource
Comments
Medline ID
PubMed ID 16978644
Journal J Mol Biol
Year 2006
Volume 363
Pages 520-30
Authors Newman JA, Das SK, Sedelnikova SE, Rice DW
Title The crystal structure of an ADP complex of Bacillus subtilis pyridoxal kinase provides evidence for the parallel emergence of enzyme activity during evolution.
Related PDB 2i5b
Related UniProtKB

Comments
This enzyme belongs to the ribokinase superfamily (EC 2.7.1.15, S00534 & S00541 in EzCatDB)(see [3]). In particular, this enzyme is homologous to HMP kinase (S00705 in EzCatDB).
According to the literature [7], Cys216 is too weak to act as a general base. The reaction mechanism must be similar to that of HMP kinase (see S00705).
Thus, this enzyme catalyzes the following reaction (see [7]):
(0) Magnesium ion, which is bound to Asp107, Glu144 and mainchain carbonyl oxygen of Thr139, coordinates with both the alpha- and beta-phosphate groups of ATP, thereby stabilizing ADP as a leaving group. Moreover, anion hole composed of mainchain amide groups of Gly213-Ala214-Gly215-Cys216 stabilizes the beta- and gamma-phosphate groups, whereas sidechain of Lys182 may stabilize alpha- and beta-phosphate groups. Thereby, the transition state in the reaction can be stabilized.
(1) An oxygen atom of gamma-phosphate group of ATP acts as a general base to deprotonate the hydroxyl group of pyridoxal.
(2) The activated hydroxyl oxygen of pyridoxal makes a nucleophilic attack on the gamma-phosphate of ATP, to produce pyridoxal phosphate. This reaction proceeds via SN2 mechanism.

Created Updated
2009-08-28 2011-11-22