2D2I

Crystal Structure of NADP-Dependent Glyceraldehyde-3-Phosphate Dehydrogenase from Synechococcus Sp. complexed with Nadp+

Summary for 2D2I

• Entry DOI: 10.2210/pdb2d2i/pdb
• Descriptor: glyceraldehyde 3-phosphate dehydrogenase, SULFATE ION, NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE, ... (4 entities in total)
• Functional Keywords: glyceraldehyde 3-phosphate dehydrogenase, rossmann fold, protein-nadp+ complex, oxidoreductase
• Biological source: Synechococcus sp.
• Total number of polymer chains: 6
• Total formula weight: 253916.60

Authors

Kitatani, T.,Nakamura, Y.,Wada, K.,Kinoshita, T.,Tamoi, M.,Shigeoka, S.,Tada, T. (deposition date: 2005-09-09, release date: 2006-07-11, Last modification date: 2024-03-13)

Primary citation

Kitatani, T.,Nakamura, Y.,Wada, K.,Kinoshita, T.,Tamoi, M.,Shigeoka, S.,Tada, T.
Structure of NADP-dependent glyceraldehyde-3-phosphate dehydrogenase from Synechococcus PCC7942 complexed with NADP
Acta Crystallogr.,Sect.F, 62:315-319, 2006

PubMed Abstract: The crystal structure of NADP-dependent glyceraldehyde-3-phosphate dehydrogenase (NADP-GAPDH) from Synechococcus PCC 7942 (S. 7942) in complex with NADP was solved by molecular replacement and refined to an R factor of 19.1% and a free R factor of 24.0% at 2.5 A resolution. The overall structure of NADP-GAPDH from S. 7942 was quite similar to those of other bacterial and eukaryotic GAPDHs. The nicotinamide ring of NADP, which is involved in the redox reaction, was oriented toward the catalytic site. The 2'-phosphate O atoms of NADP exhibited hydrogen bonds to the hydroxyl groups of Ser194 belonging to the S-loop and Thr37. These residues are therefore considered to be essential in the discrimination between NADP and NAD molecules. The C-terminal region was estimated to have an extremely flexible conformation and to play an important role in the formation of the supramolecular complex phosphoribulokinase (PRK)-regulatory peptide (CP12)-GAPDH, which regulates enzyme activities.

PubMed: 16582475
DOI: 10.1107/S1744309106007378

Experimental method

X-RAY DIFFRACTION (2.5 Å)