Crystal structures of pyruvate phosphate dikinase from maize revealed an alternative conformation in the swiveling-domain motionNakanishi, T., Nakatsu, T., Matsuoka, M., Sakata, K., Kato, H.
(2005) Biochemistry 44: 1136-1144
- PubMed: 15667207
- DOI: 10.1021/bi0484522
- Primary Citation of Related Structures:
- PubMed Abstract:
- Purification, crystallization and preliminary X-ray diffraction studies on pyruvate phosphate dikinase from maize
Nakanishi, T., Ohki, Y., Oda, J., Matsuoka, M., Sakata, K., Kato, H.
(2004) Acta Crystallogr D Biol Crystallogr 60: 193
- Primary structure of maize pyruvate, orthophosphate dikinase as deduced from cDNA sequence
Matsuoka, M., Ozeki, Y., Yamamoto, N., Hirano, H., Kano-Murakami, Y., Tanaka, Y.
(1988) J Biol Chem 263: 11080
Pyruvate phosphate dikinase (PPDK) reversibly catalyzes the conversion of ATP, phosphate, and pyruvate into AMP, pyrophosphate, and phosphoenolpyruvate (PEP), respectively. Since the nucleotide binding site (in the N-terminal domain) and the pyruvate ...
Pyruvate phosphate dikinase (PPDK) reversibly catalyzes the conversion of ATP, phosphate, and pyruvate into AMP, pyrophosphate, and phosphoenolpyruvate (PEP), respectively. Since the nucleotide binding site (in the N-terminal domain) and the pyruvate/PEP binding site (in the C-terminal domain) are separated by approximately 45 A, it has been proposed that an intermediary domain, called the central domain, swivels between these remote domains to transfer the phosphate. However, no direct structural evidence for the swiveling central domain has been found. In this study, the crystal structures of maize PPDK with and without PEP have been determined at 2.3 A resolution. These structures revealed that the central domain is located near the pyruvate/PEP binding C-terminal domain, in contrast to the PPDK from Clostridium symbiosum, wherein the central domain is located near the nucleotide-binding N-terminal domain. Structural comparisons between the maize and C. symbiosum PPDKs demonstrated that the swiveling motion of the central domain consists of a rotation of at least 92 degrees and a translation of 0.5 A. By comparing the maize PPDK structures with and without PEP, we have elucidated the mode of binding of PEP to the C-terminal domain and the induced conformational changes in the central domain.
Kinetic Crystallography Research Team, Membrane Dynamics Research Group, RIKEN Harima Institute at SPring-8, 1-1-1 Kouto, Mikazuki-cho, Sayo-gun, Hyogo 679-5148, Japan.