Arrangement of the substrates at the active site of brain pyridoxal kinase

Functional significance of some particular amino acid residues in Bombyx mori pyridoxal kinase

Pyridoxal kinase (PLK; EC 2.7.1.35) is a key enzyme for vitamin B(6) metabolism in animals. It catalyzes the ATP-dependent phosphorylation of pyridoxal, generating pyridoxal 5'-phosphate, an important cofactor for many enzymatic reactions. Bombyx mori PLK (BmPLK) is 10 or more residues shorter than mammalian PLKs, and some amino acid residues conserved in the PLKs from mammals are not maintained in the protein. Multiple sequence alignment suggested that amino acid residues Thr(47), Ile(54), Arg(88), Asn(121) and Glu(230) might play important roles in BmPLK. In this study, we used a site-directed specific mutagenesis approach to determine the functional significance of these particular amino acid residues in BmPLK. Our results demonstrated that the mutation of Asn(121) to Glu did not affect the catalytic function of BmPLK. The corresponding site-directed mutants of Thr(47) to Asn, Ile(54) to Phe, and Arg(88) to Ile displayed a decreased catalytic efficiency and an elevated Km value for substrate relative to the wild-type value, and no enzyme activity could be detected in mutant of Trp(230) to Glu. Circular dichroism analysis revealed that the mutation of Trp(230) to Glu resulted in mis-folding of the protein. Our results provided direct evidence that residue Trp(230) is crucial to maintain the structural and functional integrity of BmPLK. This study will add to the existing understanding of the characteristic of structure and function of BmPLK.

Crystal structure of brain pyridoxal kinase, a novel member of the ribokinase superfamily

The three-dimensional structures of brain pyridoxal kinase and its complex with the nucleotide ATP have been elucidated in the dimeric form at 2.1 and 2.6 A, respectively. Results have shown that pyridoxal kinase, as an enzyme obeying random sequential kinetics in catalysis, does not possess a lid shape structure common to all kinases in the ribokinase superfamily. This finding has been shown to be in line with the condition that pyridoxal kinase binds substrates with variable sizes of chemical groups at position 4 of vitamin B(6) and its derivatives. In addition, the enzyme contains a 12-residue peptide loop in the active site for the prevention of premature hydrolysis of ATP. Conserved amino acid residues Asp(118) and Tyr(127) in the peptide loop could be moved to a position covering the nucleotide after its binding so that its chance to hydrolyze in the aqueous environment of the active site was reduced. With respect to the evolutionary trend of kinase enzymes, the existence of this loop in pyridoxal kinase could be classified as an independent category in the ribokinase superfamily according to the structural feature found and mechanism followed in catalysis.

Characterization of Trypanosoma brucei pyridoxal kinase: purification, gene isolation and expression in Escherichia coli

Pyridoxal kinase catalyzes the ATP-dependent phosphorylation of vitamin B6, generating pyridoxal-5'-phosphate, an important cofactor for many enzymatic reactions. Pyridoxal kinase was purified 4300-fold to homogeneity from Trypanosoma brucei and peptides generated by proteolysis were subjected to amino acid sequence analysis. The peptide sequence information was used to generate a partial clone of T. brucei pyridoxal kinase by polymerase chain reaction (PCR), which in turn was used to screen a T. brucei genomic library for a full length clone. The 903-bp gene was sequenced and found to encode a 300-amino acid protein. The deduced amino acid sequence contains all of the peptide sequences obtained from the proteolytic cleavage of the native enzyme and shares 28% sequence identity with a putative Escherichia coli pyridoxal kinase, identified for its ability to compliment pyridoxal kinase deficient cells. The T. brucei pyridoxal kinase gene was expressed in E. coli and the purified enzyme was found to have pyridoxal kinase activity, confirming that this gene encodes the functional T. brucei enzyme. Native and recombinant pyridoxal kinase have a monomer molecular weight of 37 kDa by SDS-polyacrylamide gel electrophoresis (SDS-PAGE) and are dimers in solution. Native T. brucei pyridoxal kinase catalyzes the phosphorylation of pyridoxal with a specific activity of 990 nmol min(-1) per mg and apparent Km values for pyridoxal and ATP of 22 and 9 microM. respectively. Substrate inhibition is observed for pyridoxal. Similar results were obtained for the recombinant enzyme.

The complete 1H NMR assignments of aminoglycoside antibiotics and conformational studies of butirosin A through the use of 2D NMR spectroscopy

The complete proton assignments of the aminoglycoside antibiotics, butirosin A, kanamycin A and kanamycin B, at pH 6.5 have been made through the use of various homonuclear and heteronuclear 2D NMR methods. Butirosin A NOESY experiments suggest a stacking arrangement between the xylose and 2,6-diamino-2,6-dideoxyglucose rings, while the 2-deoxystreptamine ring and its substituent, the (S)-4-amino-2-hydroxybutyryl group, extend away from the stacked rings. Informative long-range NOEs were observed for butirosin A but not with kanamycin A or kanamycin B. Many intra-ring NOEs were observed with all three aminoglycosides that confirm the proton assignments made in this study.