New insights into the binding mode of coenzymes: structure of Thermus thermophilus Delta1-pyrroline-5-carboxylate dehydrogenase complexed with NADP+

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2007 Jun 1;63(Pt 6):462-5. doi: 10.1107/S1744309107021422. Epub 2007 May 5.

Abstract

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(+).

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • 1-Pyrroline-5-Carboxylate Dehydrogenase / chemistry
  • 1-Pyrroline-5-Carboxylate Dehydrogenase / metabolism*
  • Bacterial Proteins / chemistry
  • Bacterial Proteins / metabolism
  • Binding Sites / physiology
  • Coenzymes / chemistry
  • Coenzymes / metabolism*
  • Crystallography, X-Ray
  • Glutamate Dehydrogenase (NADP+) / chemistry
  • Glutamate Dehydrogenase (NADP+) / metabolism*
  • NADP / chemistry
  • NADP / metabolism
  • Thermus thermophilus / enzymology*

Substances

  • Bacterial Proteins
  • Coenzymes
  • NADP
  • 1-Pyrroline-5-Carboxylate Dehydrogenase
  • Glutamate Dehydrogenase (NADP+)

Associated data

  • PDB/2EHQ