PDBsum entry 1dss

Active-site carboxymethylation

PDB id: 1dss

Contents

Protein chains

333 a.a. *

Ligands

SO4 ×4

NAD ×2

Waters ×400

* Residue conservation analysis

PDB id:

1dss

Name:

Active-site carboxymethylation

Title:

Structure of active-site carboxymethylated d-glyceraldehyde-3- phosphate dehydrogenase from palinurus versicolor

Structure:

D-glyceraldehyde-3-phosphate-dehydrogenase. Chain: g, r. Fragment: NAD+ binding domain and catalytic domain. Other_details: NAD+

Source:

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

Biol. unit:

Tetramer (from PQS)

Resolution:

1.88Å R-factor: 0.172 R-free: 0.218

Authors:

S.Song,Z.Lin

Key ref:

S.Y.Song et al. (1999). Structure of active site carboxymethylated D-glyceraldehyde-3-phosphate dehydrogenase from Palinurus versicolor. J Mol Biol, 287, 719-725. PubMed id: 10191140 DOI: 10.1006/jmbi.1999.2628

Date:

04-Jun-97 Release date: 09-Dec-98

Protein chains

P56649  (G3P_PANVR) -  Glyceraldehyde-3-phosphate dehydrogenase from Panulirus versicolor

Seq: 333 a.a.

Struc: 333 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

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⁺

D-glyceraldehyde 3-phosphate + phosphate (Bound ligand (Het Group name = NAD) corresponds exactly) + NAD(+) = (2R)-3-phospho- glyceroyl phosphate + NADH + H(+)

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

reference

DOI no: 10.1006/jmbi.1999.2628

J Mol Biol 287:719-725 (1999)

PubMed id: 10191140

Structure of active site carboxymethylated D-glyceraldehyde-3-phosphate dehydrogenase from Palinurus versicolor.

S.Y.Song, Y.B.Xu, Z.J.Lin, C.L.Tsou.

ABSTRACT

The structure of active site carboxymethylated D-glyceraldehyde-3-phosphate dehydrogenase from Palinurus versicolor was determined in the presence of coenzyme NAD+ at 1.88 A resolution with a final R-factor of 0.175. The structure refinement was carried out on the basis of the structure of holo-GAPDH at 2.0 A resolution using the program XPLOR. The carboxymethyl group connected to Cys149 is stabilized by a hydrogen bond between its OZ1 and Cys149N, and charge interaction between the carboxyl group and the nicotinamide moiety. The modification of Cys149 induced conformational changes in the active site, in particular, the site of sulphate ion 501 (the proposed attacking inorganic phosphate ion in catalysis), and segment 208-218 nearby. Extensive hydrogen-bonding interactions occur in the active site, which contribute to the higher stability of the modified enzyme. The modification of the active site did not affect the conformation of GAPDH elsewhere, including the subunit interfaces. The structures of the green and red subunits in the asymmetric unit are nearly identical, suggesting that the half-site reactivity of this enzyme is from ligand-induced rather than pre-existing asymmetry. It is proposed that the carboxymethyl group takes the place of the acyl group of the reaction intermediate, and the catalytic mechanism of this enzyme is discussed in the light of a comparison of the structures of the native and the carboxymethylated GAPDH.

Selected figure(s)

Figure 2.
Figure 2. Stereoscopic view showing the carboxymethyl group in the active site and corresponding (F[o] – F[c]) electron density map.

Figure 4.
Figure 4. Model building of the hemithioacetal reaction intermediate in PV GAPDH.

The above figures are reprinted by permission from Elsevier: J Mol Biol (1999, 287, 719-725) copyright 1999.

Figures were selected by an automated process.