7C7K

Crystal Structure of Thioacyl-Glyceraldehyde-3-phosphate dehydrogenase 1(GAPDH 1) from Escherichia coli at 1.77 Angstrom resolution

Summary for 7C7K

• Entry DOI: 10.2210/pdb7c7k/pdb
• Descriptor: Glyceraldehyde-3-phosphate dehydrogenase, GLYCERALDEHYDE-3-PHOSPHATE, PHOSPHATE ION, ... (8 entities in total)
• Functional Keywords: ecgapdh 1, nad, oxidoreductase
• Biological source: Escherichia coli BL21(DE3)
• Total number of polymer chains: 4
• Total formula weight: 154880.00

Authors

Zhang, L.,Liu, M.R.,Bao, L.Y.,Yao, Y.C.,Bostrom, I.K.,Wang, Y.D.,Chen, A.Q.,Li, J.X.,Gu, S.H.,Ji, C.N. (deposition date: 2020-05-26, release date: 2021-05-26, Last modification date: 2024-10-16)

Primary citation

Zhang, L.,Liu, M.,Bao, L.,Bostrom, K.I.,Yao, Y.,Li, J.,Gu, S.,Ji, C.
Novel Structures of Type 1 Glyceraldehyde-3-phosphate Dehydrogenase from Escherichia coli Provide New Insights into the Mechanism of Generation of 1,3-Bisphosphoglyceric Acid.
Biomolecules, 11:-, 2021

PubMed Abstract: Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a highly conserved enzyme involved in the ubiquitous process of glycolysis and presents a loop (residues 208-215 of GAPDH) in two alternative conformations (I and II). It is uncertain what triggers this loop rearrangement, as well as which is the precise site from which phosphate attacks the thioacyl intermediate precursor of 1,3-bisphosphoglycerate (BPG). To clarify these uncertainties, we determined the crystal structures of complexes of wild-type GAPDH (WT) with NAD and phosphate or G3P, and of essentially inactive GAPDH mutants (C150S, H177A), trapping crystal structures for the thioacyl intermediate or for ternary complexes with NAD and either phosphate, BPG, or G3P. Analysis of these structures reported here lead us to propose that phosphate is located in the "new Pi site" attacks the thioester bond of the thioacyl intermediate to generate 1,3-bisphosphoglyceric acid (BPG). In the structure of the thioacyl intermediate, the mobile loop is in conformation II in subunits O, P, and R, while both conformations coexist in subunit Q. Moreover, only the Q subunit hosts bound NADH. In the R subunit, only the pyrophosphate part of NADH is well defined, and NADH is totally absent from the O and P subunits. Thus, the change in loop conformation appears to occur after NADH is produced, before NADH is released. In addition, two new D-glyceraldehyde-3-phosphate (G3P) binding forms are observed in WT.NAD.G3P and C150A+H177A.NAD.G3P. In summary, this paper improves our understanding of the GAPDH catalytic mechanism, particularly regarding BPG formation.

PubMed: 34827563
DOI: 10.3390/biom11111565

Experimental method

X-RAY DIFFRACTION (1.77 Å)