New insights into the binding mode of coenzymes: structure of Thermus thermophilus Delta1-pyrroline-5-carboxylate dehydrogenase complexed with NADP+.
Delta(1)-Pyrroline-5-carboxylate dehydrogenase (P5CDh) is known to preferentially use NAD(+) as a coenzyme. The k(cat) value of Thermus thermophilus P5CDh (TtP5CDh) is four times lower for NADP(+) than for NAD(+). The crystal structure of NADP(+)-bound TtP5CDh 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 TtP5CDh and NADP(+) compared with that between TtP5CDh 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(+).
Inagaki
Eiji
E
RIKEN SPring-8 Center, Harima Institute, Japan.
Ohshima
Noriyasu
N
Sakamoto
Keiko
K
Babayeva
Nigar D
ND
Kato
Hiroaki
H
Yokoyama
Shigeyuki
S
Tahirov
Tahir H
TH
D050842:1-Pyrroline-5-Carboxylate Dehydrogenase / Q000737:chemistry / Q000378:metabolism*; D001426:Bacterial Proteins / Q000737:chemistry / Q000378:metabolism; D001665:Binding Sites / Q000502:physiology; D003067:Coenzymes / Q000737:chemistry / Q000378:metabolism*; D018360:Crystallography, X-Ray; D018086:Glutamate Dehydrogenase (NADP+) / Q000737:chemistry / Q000378:metabolism*; D009249:NADP / Q000737:chemistry / Q000378:metabolism; D016963:Thermus thermophilus / Q000201:enzymology*
D001426:Bacterial Proteins; D003067:Coenzymes; D009249:NADP; D050842:1-Pyrroline-5-Carboxylate Dehydrogenase; D018086:Glutamate Dehydrogenase (NADP+)