PDBsum entry: 1ihx

Oxidoreductase

PDB id: 1ihx

Contents

Protein chains

333 a.a. *

Ligands

SO4 ×8

SND ×4

Waters ×228

* Residue conservation analysis

PDB id:

1ihx

Name:

Oxidoreductase

Title:

Crystal structure of two d-glyceraldehyde-3-phosphate dehydrogenase complexes: a case of asymmetry

Structure:

Glyceraldehyde 3-phosphate dehydrogenase. Chain: a, b, c, d. Synonym: gapdh. Ec: 1.2.1.12

Source:

Palinurus versicolor. South china sea lobster. Organism_taxid: 82835. Tissue: tail muscle

Biol. unit:

Tetramer (from PQS)

Resolution:

2.80Å R-factor: 0.177 R-free: 0.204

Authors:

Y.-Q.Shen,S.-Y.Song,Z.-J.Lin

Key ref:

Y.Q.Shen et al. (2002). Structures of D-glyceraldehyde-3-phosphate dehydrogenase complexed with coenzyme analogues. Acta Crystallogr D Biol Crystallogr, 58, 1287-1297. PubMed id: 12136140 DOI: 10.1107/S090744490200999X

Date:

20-Apr-01 Release date: 31-Jul-02

Protein chains

P56649  (G3P_PANVR) -  Glyceraldehyde-3-phosphate dehydrogenase

Seq: 333 a.a.

Struc: 333 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.1.2.1.12 - Glyceraldehyde-3-phosphate dehydrogenase (phosphorylating).
• Pathway: Glyceraldehyde-3-phosphate Dehydrogenase (phosphorylating)
• Reaction: D-glyceraldehyde 3-phosphate + phosphate + NAD⁺ = 3-phospho-D-glyceroyl phosphate + NADH

D-glyceraldehyde 3-phosphate + phosphate + NAD(+) (Bound ligand (Het Group name = SND) matches with 81.00% similarity) = 3-phospho-D-glyceroyl phosphate + NADH

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 Gene Ontology (GO) functional annotation 

• Cellular component: cytoplasm (1 term)
• Biological process: oxidation-reduction process (3 terms)
• Biochemical function: nucleotide binding (6 terms)

reference

DOI no: 10.1107/S090744490200999X

Acta Crystallogr D Biol Crystallogr 58:1287-1297 (2002)

PubMed id: 12136140

Structures of D-glyceraldehyde-3-phosphate dehydrogenase complexed with coenzyme analogues.

Y.Q.Shen, S.Y.Song, Z.J.Lin.

ABSTRACT

Crystal structures of GAPDH from Palinurus versicolor complexed with two coenzyme analogues, SNAD(+) and ADP-ribose, were determined by molecular replacement and refined at medium resolution to acceptable crystallographic factors and reasonable stereochemistry. ADP-ribose in the ADP-ribose-GAPDH complex adopts a rather extended conformation. The interactions between ADP-ribose and GAPDH are extensive and in a fashion dissimilar to the coenzyme NAD(+). This accounts for the strong inhibiting ability of ADP-ribose. The conformational changes induced by ADP-ribose binding are quite different to those induced by NAD(+) binding. This presumably explains the non-cooperative behaviour of the ADP-ribose binding. Unexpectedly, the SNAD(+)-GAPDH complex reveals pairwise asymmetry. The asymmetry is significant, including the SNAD(+) molecule, active-site structure and domain motion induced by the coenzyme analogue. In the yellow or red subunits [nomenclature of subunits is as in Buehner et al. (1974). J. Mol. Biol. 90, 25-49], SNAD(+) binds similarly, as does NAD(+) in holo-GAPDH. While, in the green or blue subunit, the SNAD(+) binds in a non-productive manner, resulting in a disordered thionicotinamide ring and rearranged active-site residues. The conformation seen in the yellow and red subunits of SNAD(+)-GAPDH is likely to represent the functional state of the enzyme complex in solution and thus accounts for the substrate activity of SNAD(+). A novel type of domain motion is observed for the binding of the coenzyme analogues to GAPDH. The possible conformational transitions involved in the coenzyme binding and the important role of the nicotinamide group are discussed.

Selected figure(s)

Figure 2.
Figure 2 The conformational comparison of ADP-ribose (green) and NAD^+ (purple) in GAPDH. The conformations of ADP-ribose (yellow) and NAD^+ (red) in ADH are also included.

Figure 4.
Figure 4 The conformations of ADP-ribose (green) and NAD+ (purple) in GAPDH. As a comparison, the conformations of ADP-ribose (yellow) and NAD^+ (red) in ADH (pdb codes: [163]5adh and [164]6adh , Eklund et al., 1984[165] [Eklund, H., Samama, J. P. & Jones, T. A. (1984). Biochemistry, 23, 5982-5996.]-[166][bluearr.gif] ) are also included.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2002, 58, 1287-1297) copyright 2002.

Figures were selected by an automated process.