Open AccessNew insights into the binding mode of coenzymes: structure of Thermus thermophilus Δ 1 ‐pyrroline‐5‐carboxylate dehydrogenase complexed with NADP +
Author(s) -
Inagaki Eiji,
Ohshima Noriyasu,
Sakamoto Keiko,
Babayeva Nigar D.,
Kato Hiroaki,
Yokoyama Shigeyuki,
Tahirov Tahir H.
Publication year - 2007
Publication title -
acta crystallographica section f
Language(s) - English
Resource type - Journals
ISSN - 1744-3091
DOI - 10.1107/s1744309107021422
Subject(s) - nad+ kinase , thermus thermophilus , cofactor , stereochemistry , steric effects , carboxylate , dehydrogenase , chemistry , crystallography , enzyme , biochemistry , escherichia coli , gene
Δ 1 ‐Pyrroline‐5‐carboxylate dehydrogenase (P5CDh) is known to preferentially use NAD + as a coenzyme. The k cat value of Thermus thermophilus P5CDh ( Tt P5CDh) is four times lower for NADP + than for NAD + . The crystal structure of NADP + ‐bound Tt P5CDh was solved in order to study the structure–activity relationships for the coenzymes. The binding mode of NADP + is essentially identical to that in the previously solved NAD + ‐bound form, except for the regions around the additional 2′‐phosphate group of NADP + . The coenzyme‐binding site can only accommodate this group by the rotation of a glutamate residue and subtle shifts in the main chain. The 2′‐phosphate of NADP + increases the number of hydrogen bonds between Tt P5CDh and NADP + compared with that between Tt P5CDh and NAD + . Furthermore, the phosphate of the bound NADP + would restrict the `bending' of the coenzyme because of steric hindrance. Such bending is important for dissociation of the coenzymes. These results provide a plausible explanation of the lower turnover rate of NADP + compared with NAD + .