PDBsum entry 2id2

Oxidoreductase

PDB id: 2id2

Contents

Protein chains

473 a.a. *

Ligands

SO4 ×7

NAP ×4

Waters ×1109

* Residue conservation analysis

PDB id:

2id2

Name:

Oxidoreductase

Title:

Gapn t244s mutant x-ray structure at 2.5 a

Structure:

NADP-dependent glyceraldehyde-3-phosphate dehydrogenase. Chain: a, b, c, d. Synonym: non-phosphorylating glyceraldehyde 3-phosphate dehydrogenase, glyceraldehyde-3-phosphate dehydrogenase [nadp+], triosephosphate dehydrogenase. Engineered: yes. Mutation: yes

Source:

Streptococcus mutans. Organism_taxid: 1309. Strain: clarke 1924. Gene: gapn. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.50Å R-factor: 0.176 R-free: 0.227

Authors:

A.Pailot,K.D'Ambrosio,C.Corbier,F.Talfournier,G.Branlant

Key ref:

A.Pailot et al. (2006). Invariant Thr244 is essential for the efficient acylation step of the non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase from Streptococcus mutans. Biochem J, 400, 521-530. PubMed id: 16958622

Date:

14-Sep-06 Release date: 18-Sep-07

Protein chains

Q59931  (GAPN_STRMU) -  NADP-dependent glyceraldehyde-3-phosphate dehydrogenase from Streptococcus mutans serotype c (strain ATCC 700610 / UA159)

Seq: 475 a.a.

Struc: 473 a.a.*

* PDB and UniProt seqs differ at 4 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.1.2.1.9 - glyceraldehyde-3-phosphate dehydrogenase (NADP(+)).
• Reaction: D-glyceraldehyde 3-phosphate + NADP⁺ + H2O = (2R)-3-phosphoglycerate + NADPH + 2 H⁺

D-glyceraldehyde 3-phosphate + NADP(+) + H2O (Bound ligand (Het Group name = NAP) corresponds exactly) = (2R)-3-phosphoglycerate + NADPH + 2 × H(+)

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

reference

Biochem J 400:521-530 (2006)

PubMed id: 16958622

Invariant Thr244 is essential for the efficient acylation step of the non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase from Streptococcus mutans.

A.Pailot, K.D'Ambrosio, C.Corbier, F.Talfournier, G.Branlant.

ABSTRACT

One of the most striking features of several X-ray structures of CoA-independent ALDHs (aldehyde dehydrogenases) in complex with NAD(P) is the conformational flexibility of the NMN moiety. However, the fact that the rate of the acylation step is high in GAPN (non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase) from Streptococcus mutans implies an optimal positioning of the nicotinamide ring relative to the hemithioacetal intermediate within the ternary GAPN complex to allow an efficient and stereospecific hydride transfer. Substitutions of serine for invariant Thr244 and alanine for Lys178 result in a drastic decrease of the efficiency of hydride transfer which becomes rate-limiting. The crystal structure of the binary complex T244S GAPN-NADP shows that the absence of the beta-methyl group leads to a well-defined conformation of the NMN part, including the nicotinamide ring, clearly different from that depicted to be suitable for an efficient hydride transfer in the wild-type. The approximately 0.6-unit increase in pK(app) of the catalytic Cys302 observed in the ternary complex for both mutated GAPNs is likely to be due to a slight difference in positioning of the nicotinamide ring relative to Cys302 with respect to the wild-type ternary complex. Taken together, the data support a critical role of the Thr244 beta-methyl group, held in position through a hydrogen-bond interaction between the Thr244 beta-hydroxy group and the epsilon-amino group of Lys178, in permitting the nicotinamide ring to adopt a conformation suitable for an efficient hydride transfer during the acylation step for all the members of the CoA-independent ALDH family.