PDBsum entry 1dc3

Oxidoreductase

PDB id: 1dc3

Contents

Protein chains

330 a.a. *

Waters ×207

* Residue conservation analysis

PDB id:

1dc3

Name:

Oxidoreductase

Title:

Structural analysis of glyceraldehyde 3-phosphate dehydrogenase from escherichia coli: direct evidence for substrate binding and cofactor- induced conformational changes

Structure:

Glyceraldehyde 3-phosphate dehydrogenase. Chain: a, b. Fragment: apo. Synonym: gapdh. Ec: 1.2.1.12

Source:

Escherichia coli. Organism_taxid: 562

Biol. unit:

Tetramer (from PQS)

Resolution:

2.50Å R-factor: 0.189 R-free: 0.241

Authors:

M.Yun,C.G.Park,J.Y.Kim,H.W.Park

Key ref:

M.Yun et al. (2000). Structural analysis of glyceraldehyde 3-phosphate dehydrogenase from Escherichia coli: direct evidence of substrate binding and cofactor-induced conformational changes. Biochemistry, 39, 10702-10710. PubMed id: 10978154 DOI: 10.1021/bi9927080

Date:

04-Nov-99 Release date: 23-Aug-00

Protein chains

P0A9B2  (G3P1_ECOLI) -  Glyceraldehyde-3-phosphate dehydrogenase A from Escherichia coli (strain K12)

Seq: 331 a.a.

Struc: 330 a.a.

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⁺ = (2R)-3-phospho- glyceroyl phosphate + NADH + H⁺

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

reference

DOI no: 10.1021/bi9927080

Biochemistry 39:10702-10710 (2000)

PubMed id: 10978154

Structural analysis of glyceraldehyde 3-phosphate dehydrogenase from Escherichia coli: direct evidence of substrate binding and cofactor-induced conformational changes.

M.Yun, C.G.Park, J.Y.Kim, H.W.Park.

ABSTRACT

The crystal structures of gyceraldehyde 3-phosphate dehydrogenase (GAPDH) from Escherichia coli have been determined in three different enzymatic states, NAD(+)-free, NAD(+)-bound, and hemiacetal intermediate. The NAD(+)-free structure reported here has been determined from monoclinic and tetragonal crystal forms. The conformational changes in GAPDH induced by cofactor binding are limited to the residues that bind the adenine moiety of NAD(+). Glyceraldehyde 3-phosphate (GAP), the substrate of GAPDH, binds to the enzyme with its C3 phosphate in a hydrophilic pocket, called the "new P(i)" site, which is different from the originally proposed binding site for inorganic phosphate. This observed location of the C3 phosphate is consistent with the flip-flop model proposed for the enzyme mechanism [Skarzynski, T., Moody, P. C., and Wonacott, A. J. (1987) J. Mol. Biol. 193, 171-187]. Via incorporation of the new P(i) site in this model, it is now proposed that the C3 phosphate of GAP initially binds at the new P(i) site and then flips to the P(s) site before hydride transfer. A superposition of NAD(+)-bound and hemiacetal intermediate structures reveals an interaction between the hydroxyl oxygen at the hemiacetal C1 of GAP and the nicotinamide ring. This finding suggests that the cofactor NAD(+) may stabilize the transition state oxyanion of the hemiacetal intermediate in support of the flip-flop model for GAP binding.