2EHQ

Crystal analysis of 1-pyrroline-5-carboxylate dehydrogenase from thermus with bound NADP

Summary for 2EHQ

• Entry DOI: 10.2210/pdb2ehq/pdb
• Descriptor: 1-pyrroline-5-carboxylate dehydrogenase, ACETATE ION, SODIUM ION, ... (6 entities in total)
• Functional Keywords: enzyme-coenzyme complex, structural genomics, nppsfa, national project on protein structural and functional analyses, riken structural genomics/proteomics initiative, rsgi, oxidoreductase
• Biological source: Thermus thermophilus
• Total number of polymer chains: 2
• Total formula weight: 116824.00

Authors

Inagaki, E.,Sakamoto, K.,Yokoyama, S.,RIKEN Structural Genomics/Proteomics Initiative (RSGI) (deposition date: 2007-03-07, release date: 2007-05-01, Last modification date: 2023-10-25)

Primary citation

Inagaki, E.,Ohshima, N.,Sakamoto, K.,Babayeva, N.D.,Kato, H.,Yokoyama, S.,Tahirov, T.H.
New insights into the binding mode of coenzymes: structure of Thermus thermophilus Delta1-pyrroline-5-carboxylate dehydrogenase complexed with NADP+.
Acta Crystallogr.,Sect.F, 63:462-465, 2007

PubMed 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(+).

PubMed: 17554163
DOI: 10.1107/S1744309107021422

Experimental method

X-RAY DIFFRACTION (1.55 Å)