EzCatDB: S00905
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DB codeS00905
RLCP classification3.103.78020.387 : Transfer
CATH domainDomain 13.40.1190.20 : UDP-N-acetylmuramoyl-L-alanineCatalytic domain
E.C.2.7.1.35

CATH domainRelated DB codes (homologues)
3.40.1190.20 : UDP-N-acetylmuramoyl-L-alanineS00534,S00541,S00678,S00705,S00903,S00904,S00453,D00416

Enzyme Name
UniProtKBKEGG

P39610
Protein namePhosphomethylpyrimidine kinasePyridoxal kinase
Pyridoxal kinase (phosphorylating)
Pyridoxal 5-phosphate-kinase
Pyridoxal phosphokinase
Pyridoxine kinase
SynonymsEC 2.7.4.7
HMP-phosphate kinase
HMP-P kinase
HMPP kinase
RefSeqNP_391681.1 (Protein)
NC_000964.3 (DNA/RNA sequence)
PfamPF08543 (Phos_pyr_kin)
[Graphical view]

KEGG pathways
MAP codePathways
MAP00750Vitamin B6 metabolism

UniProtKB:Accession NumberP39610
Entry namePDXK_BACSU
ActivityATP + pyridoxal = ADP + pyridoxal 5'-phosphate.
SubunitHomodimer.
Subcellular location
Cofactor

Compound table: links to PDB-related databases & PoSSuM

CofactorsSubstratesProducts
KEGG-idC00305C00002C00250C00008C00018
CompoundMagnesiumATPPyridoxalADPPyridoxal phosphate
Typedivalent metal (Ca2+, Mg2+)amine group,nucleotidearomatic ring (with nitrogen atoms),carbohydrateamine group,nucleotidearomatic ring (with nitrogen atoms),phosphate group/phosphate ion
ChEBI18420
15422
17310
16761
18405
PubChem888
5957
1050
6022
1051
             
2i5bA00UnboundUnboundUnboundBound:ADPUnbound
2i5bB00UnboundUnboundUnboundBound:ADPUnbound
2i5bC00UnboundUnboundUnboundBound:ADPUnbound
2i5bD00UnboundUnboundUnboundBound:ADPUnbound
2i5bE00UnboundUnboundUnboundBound:ADPUnbound

Active-site residues
resource
literature [6], [7]
pdbCatalytic residuesCofactor-binding residuesMain-chain involved in catalysis
           
2i5bA00LYS 182;CYS 216
ASP 107;GLU 144;THR 139(Magnesium binding)
GLY 213;ALA 214;GLY 215;CYS 216
2i5bB00LYS 182;CYS 216
ASP 107;GLU 144;THR 139(Magnesium binding)
GLY 213;ALA 214;GLY 215;CYS 216
2i5bC00LYS 182;CYS 216
ASP 107;GLU 144;THR 139(Magnesium binding)
GLY 213;ALA 214;GLY 215;CYS 216
2i5bD00LYS 182;CYS 216
ASP 107;GLU 144;THR 139(Magnesium binding)
GLY 213;ALA 214;GLY 215;CYS 216
2i5bE00LYS 182;CYS 216
ASP 107;GLU 144;THR 139(Magnesium binding)
GLY 213;ALA 214;GLY 215;CYS 216

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[6]Fig.6, p1815-1816
[7]Fig.2, p.525

references
[1]
CommentsX-RAY CRYSTALLOGRAPHY (1.84 ANGSTROMS).
PubMed ID9519409
JournalStructure
Year1998
Volume6
Pages183-93
AuthorsSigrell JA, Cameron AD, Jones TA, Mowbray SL
TitleStructure 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 PDB1rkd
Related UniProtKBP0A9J6
[2]
CommentsX-RAY CRYSTALLOGRAPHY (1.5 ANGSTROMS) IN COMPLEX WITH SUBSTRATE, HOMOTRIMERIZATION, AND MUTAGENESIS OF CYS-198.
PubMed ID10891066
JournalBiochemistry
Year2000
Volume39
Pages7868-77
AuthorsCampobasso N, Mathews II, Begley TP, Ealick SE
TitleCrystal structure of 4-methyl-5-beta-hydroxyethylthiazole kinase from Bacillus subtilis at 1.5 A resolution.
Related PDB1c3q,1esq,1esj,1ekq,1ekk
Related UniProtKBP39593
[3]
CommentsX-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF 23-266.
PubMed ID11839308
JournalStructure
Year2002
Volume10
Pages225-35
AuthorsCheng G, Bennett EM, Begley TP, Ealick SE
TitleCrystal structure of 4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate kinase from Salmonella typhimurium at 2.3 A resolution.
Related PDB1jxh,1jxi
Related UniProtKBP55882
[4]
PubMed ID14675553
JournalCurr Opin Struct Biol
Year2003
Volume13
Pages739-47
AuthorsSettembre E, Begley TP, Ealick SE
TitleStructural biology of enzymes of the thiamin biosynthesis pathway.
[5]
JournalInt J Mol Sci
Year2004
Volume5
Pages141-153
AuthorsEdyta Dyguda, Borys Szefczyk and W. A. Sokalski
TitleThe Mechanism of Phosphoryl Transfer Reaction and the Role of Active Site Residues on the Basis of Ribokinase-Like Kinases
[6]
CommentsX-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS).
PubMed ID15458630
JournalStructure
Year2004
Volume12
Pages1809-21
AuthorsZhang Y, Dougherty M, Downs DM, Ealick SE
TitleCrystal structure of an aminoimidazole riboside kinase from Salmonella enterica: implications for the evolution of the ribokinase superfamily.
Related PDB1tyy,1tz3,1tz6
Related UniProtKBQ8ZKR2
[7]
PubMed ID16978644
JournalJ Mol Biol
Year2006
Volume363
Pages520-30
AuthorsNewman JA, Das SK, Sedelnikova SE, Rice DW
TitleThe crystal structure of an ADP complex of Bacillus subtilis pyridoxal kinase provides evidence for the parallel emergence of enzyme activity during evolution.
Related PDB2i5b

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.

createdupdated
2009-08-282011-11-22


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