6K92
Pyridoxal Kinase from Leishmania donovani in complex with ADP and Ginkgotoxin
Summary for 6K92
| Entry DOI | 10.2210/pdb6k92/pdb |
| Descriptor | Pyridoxal kinase, putative, ADENOSINE-5'-DIPHOSPHATE, 5-(hydroxymethyl)-4-(methoxymethyl)-2-methylpyridin-3-ol, ... (7 entities in total) |
| Functional Keywords | nucleotide binding, atp binding, kinase activity, metal binding, transferase |
| Biological source | Leishmania donovani (strain BPK282A1) |
| Total number of polymer chains | 2 |
| Total formula weight | 72410.34 |
| Authors | Are, S.,Gatreddi, S.,Qureshi, I.A. (deposition date: 2019-06-13, release date: 2020-03-25, Last modification date: 2024-03-27) |
| Primary citation | Are, S.,Gatreddi, S.,Jakkula, P.,Qureshi, I.A. Structural attributes and substrate specificity of pyridoxal kinase from Leishmania donovani. Int.J.Biol.Macromol., 152:812-827, 2020 Cited by PubMed Abstract: The enzyme pyridoxal kinase (PdxK) catalyzes the conversion of pyridoxal to pyridoxal-5'-phosphate (PLP) using ATP as the co-factor. The product pyridoxal-5'-phosphate plays a key role in several biological processes such as transamination, decarboxylation and deamination. In the present study, full-length ORF of PdxK from Leishmania donovani (LdPdxK) was cloned and then purified using affinity chromatography. LdPdxK exists as a homo-dimer in solution and shows more activity at near to physiological pH. Biochemical analysis of LdPdxK with pyridoxal, pyridoxamine, pyridoxine and ginkgotoxin revealed its affinity preference towards different substrates. The secondary structure analysis using circular dichroism spectroscopy showed LdPdxK to be predominantly α-helical in organization which tends to decline at lower and higher pH. Simultaneously, LdPdxK was crystallized and its three-dimensional structure in complex with ADP and different substrates were determined. Crystal structure of LdPdxK delineated that it has a central core of β-sheets surrounded by α-helices with a conserved GTGD ribokinase motif. The structures of LdPdxK disclosed no major structural changes between ADP and ADP- substrate bound structures. In addition, comparative structural analysis highlighted the key differences between the active site pockets of leishmanial and human PdxK, rendering LdPdxK an attractive candidate for the designing of novel and specific inhibitors. PubMed: 32105687DOI: 10.1016/j.ijbiomac.2020.02.257 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.85 Å) |
Structure validation
Download full validation report
