1RFV

Crystal structure of pyridoxal kinase complexed with ADP

Summary for 1RFV

• Entry DOI: 10.2210/pdb1rfv/pdb
• Related: 1LHP 1LHR 1RFT 1RFU
• Descriptor: pyridoxal kinase, ZINC ION, ADENOSINE-5'-DIPHOSPHATE, ... (4 entities in total)
• Functional Keywords: transferase
• Biological source: Ovis aries (sheep)
• Cellular location: Cytoplasm: P82197
• Total number of polymer chains: 2
• Total formula weight: 70706.98

Authors

Liang, D.-C.,Jiang, T.,Li, M.-H. (deposition date: 2003-11-10, release date: 2004-04-27, Last modification date: 2023-10-25)

Primary citation

Li, M.-H.,Kwok, F.,Chang, W.-R.,Liu, S.-Q.,Lo, S.C.L.,Zhang, J.-P.,Jiang, T.,Liang, D.-C.
Conformational changes in the reaction of pyridoxal kinase
J.BIOL.CHEM., 279:17459-17465, 2004

PubMed Abstract: To understand the processes involved in the catalytic mechanism of pyridoxal kinase (PLK),1 we determined the crystal structures of PLK.AMP-PCP-pyridoxamine, PLK.ADP.PLP, and PLK.ADP complexes. Comparisons of these structures have revealed that PLK exhibits different conformations during its catalytic process. After the binding of AMP-PCP (an analogue that replaced ATP) and pyridoxamine to PLK, this enzyme retains a conformation similar to that of the PLK.ATP complex. The distance between the reacting groups of the two substrates is 5.8 A apart, indicating that the position of ATP is not favorable to spontaneous transfer of its phosphate group. However, the structure of PLK.ADP.PLP complex exhibited significant changes in both the conformation of the enzyme and the location of the ligands at the active site. Therefore, it appears that after binding of both substrates, the enzyme-substrate complex requires changes in the protein structure to enable the transfer of the phosphate group from ATP to vitamin B(6). Furthermore, a conformation of the enzyme-substrate complex before the transition state of the enzymatic reaction was also hypothesized.

PubMed: 14722069
DOI: 10.1074/jbc.M312380200

Experimental method

X-RAY DIFFRACTION (2.8 Å)