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

References listed in PDB file

Key reference

Title

Structure of active site carboxymethylated d-Glyceraldehyde-3-Phosphate dehydrogenase from palinurus versicolor.

Authors

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

Ref.

J Mol Biol, 1999, 287, 719-725. [DOI no: 10.1006/jmbi.1999.2628]

PubMed id

10191140

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.

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.

Secondary reference #1

Title

Structure of d-Glyceraldehyde-3-Phosphate dehydrogenase from palinurus versicolor carrying the fluorescent NAD derivatives at 2.7 a resolution.

Authors

Z.J.Lin, J.Li, F.M.Zhang, S.Y.Song, J.Yang, S.J.Liang, C.L.Tsou.

Ref.

Arch Biochem Biophys, 1993, 302, 161-166.

PubMed id

8470893

Secondary reference #2

Title

Preliminary crystallographic studies of lobster d-Glyceraldehyde-3-Phosphate dehydrogenase and the modified enzyme carrying the fluorescent derivative.

Authors

S.Y.Song, Y.G.Gao, J.M.Zhou, C.L.Tsou.

Ref.

J Mol Biol, 1983, 171, 225-228. [DOI no: 10.1016/S0022-2836(83)80355-6]

PubMed id

6655693

Figure 1.
FIo. 1. A comparison of the precession photographs of native, carboxymethylated and fluorescent derivative of v-glyceraldehyde-3-phosphate dehydrogenase. (a)Native enzyme, hO1; (b)native enzyme, hk0; (c) carboxymethylated enzyme, hk0; (d) enzyme carrying the fluorescent derivative, hk0.

The above figure is reproduced from the cited reference with permission from Elsevier