EzCatDB: S00903
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DB codeS00903
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,S00904,S00905,S00453,D00416

Enzyme Name
UniProtKBKEGG

P40191
Protein namePyridoxine kinasePyridoxal kinase
Pyridoxal kinase (phosphorylating)
Pyridoxal 5-phosphate-kinase
Pyridoxal phosphokinase
Pyridoxine kinase
SynonymsEC 2.7.1.35
Pyridoxal kinase
Vitamin B6 kinase
Pyridoxamine kinase
PN/PL/PM kinase
RefSeqNP_416913.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_490654.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
PfamPF08543 (Phos_pyr_kin)
[Graphical view]

KEGG pathways
MAP codePathways
MAP00750Vitamin B6 metabolism

UniProtKB:Accession NumberP40191
Entry namePDXK_ECOLI
ActivityATP + pyridoxal = ADP + pyridoxal 5'-phosphate.
Subunit
Subcellular location
CofactorZinc or magnesium.

Compound table: links to PDB-related databases & PoSSuM

CofactorsSubstratesProducts
KEGG-idC00305C00038C00238C00002C00250C00008C00018
CompoundMagnesiumZincPotassiumATPpyridoxalADPpyridoxal 5'-phosphate
Typedivalent metal (Ca2+, Mg2+)heavy metalunivalent metal (Na+, K+)amine group,nucleotidearomatic ring (with nitrogen atoms),carbohydrateamine group,nucleotidearomatic ring (with nitrogen atoms),phosphate group/phosphate ion
ChEBI18420
29105
29103
15422
17310
16761
18405
PubChem888
32051
813
5957
1050
6022
1051
               
2ddmA00UnboundUnboundUnboundUnboundUnboundUnboundUnbound
2ddmB00UnboundUnboundUnboundUnboundUnboundUnboundUnbound
2ddoA00Bound:_MGUnboundUnboundBound:ATPUnboundUnboundUnbound
2ddoB00UnboundUnboundUnboundUnboundUnboundUnboundUnbound
2ddwA00UnboundUnboundUnboundUnboundBound:PXLUnboundUnbound
2ddwB00UnboundUnboundUnboundUnboundBound:PXLUnboundUnbound

Active-site residues
resource
literature [4], [6], [8], [9], [12]
pdbCatalytic residuesCofactor-binding residuesMain-chain involved in catalysis
           
2ddmA00ASP 233
TYR 136;GLU 162(Magnesium binding)
GLY 230;THR 231;GLY 232
2ddmB00ASP 233
TYR 136;GLU 162(Magnesium binding)
GLY 230;THR 231;GLY 232
2ddoA00ASP 233
TYR 136;GLU 162(Magnesium binding)
GLY 230;THR 231;GLY 232
2ddoB00ASP 233
TYR 136;GLU 162(Magnesium binding)
GLY 230;THR 231;GLY 232
2ddwA00ASP 233
TYR 136;GLU 162(Magnesium binding)
GLY 230;THR 231;GLY 232
2ddwB00ASP 233
TYR 136;GLU 162(Magnesium binding)
GLY 230;THR 231;GLY 232

References for Catalytic Mechanism
ReferencesSectionsNo. 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]
PubMed ID9252787
JournalEnzyme Protein
Year1996
Volume49
Pages291-304
AuthorsLaine-Cessac P, Allain P
TitleKinetic studies of the effects of K+, Na+ and Li+ on the catalytic activity of human erythrocyte pyridoxal kinase.
[2]
PubMed ID9843365
JournalBiochemistry
Year1998
Volume37
Pages15607-20
AuthorsMathews II, Erion MD, Ealick SE
TitleStructure of human adenosine kinase at 1.5 A resolution.
[3]
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.
[4]
CommentsX-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) IN COMPLEX WITH SUBSTRATE; ADP AND COFACTOR.
PubMed ID12235162
JournalJ Biol Chem
Year2002
Volume277
Pages46385-90
AuthorsLi MH, Kwok F, Chang WR, Lau CK, Zhang JP, Lo SC, Jiang T, Liang DC
TitleCrystal structure of brain pyridoxal kinase, a novel member of the ribokinase superfamily.
Related PDB1lhp,1lhr
Related UniProtKBP82197
[5]
CommentsX-RAY CRYSTALLOGRAPHY (2.22 ANGSTROMS) OF 2-287, SUBUNIT.
PubMed ID15547280
JournalJ Bacteriol
Year2004
Volume186
Pages8074-82
AuthorsSafo MK, Musayev FN, Hunt S, di Salvo ML, Scarsdale N, Schirch V
TitleCrystal structure of the PdxY Protein from Escherichia coli.
Related PDB1td2
Related UniProtKBP77150
[6]
PubMed ID14722069
JournalJ Biol Chem
Year2004
Volume279
Pages17459-65
AuthorsLi MH, Kwok F, Chang WR, Liu SQ, Lo SC, Zhang JP, Jiang T, Liang DC
TitleConformational changes in the reaction of pyridoxal kinase.
Related PDB1rft,1rfu,1rfv
[7]
PubMed ID15985434
JournalJ Biol Chem
Year2005
Volume280
Pages31220-9
AuthorsTang 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
TitleCrystal structure of pyridoxal kinase in complex with roscovitine and derivatives.
Related PDB1ygk,1ygj,1yhj
[8]
PubMed ID16740960
JournalJ Bacteriol
Year2006
Volume188
Pages4542-52
AuthorsSafo MK, Musayev FN, di Salvo ML, Hunt S, Claude JB, Schirch V
TitleCrystal structure of pyridoxal kinase from the Escherichia coli pdxK gene: implications for the classification of pyridoxal kinases.
Related PDB2ddm,2ddo,2ddw
[9]
PubMed ID16267046
JournalJ Biol Chem
Year2006
Volume281
Pages1305-8
AuthorsDi Cera E
TitleA structural perspective on enzymes activated by monovalent cations.
[10]
PubMed ID17015484
JournalPhysiol Rev
Year2006
Volume86
Pages1049-92
AuthorsPage MJ, Di Cera E
TitleRole of Na+ and K+ in enzyme function.
[11]
PubMed ID17766369
JournalProtein Sci
Year2007
Volume16
Pages2184-94
AuthorsMusayev FN, di Salvo ML, Ko TP, Gandhi AK, Goswami A, Schirch V, Safo MK
TitleCrystal Structure of human pyridoxal kinase: structural basis of M(+) and M(2+) activation.
Related PDB2yxt,2yxu
[12]
PubMed ID19351586
JournalBiochem Biophys Res Commun
Year2009
Volume381
Pages12-5
AuthorsGandhi AK, Ghatge MS, Musayev FN, Sease A, Aboagye SO, di Salvo ML, Schirch V, Safo MK
TitleKinetic and structural studies of the role of the active site residue Asp235 of human pyridoxal kinase.
Related PDB3fhx,3fhy

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.

createdupdated
2009-08-242012-01-12


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Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2012 - March 2013)
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