1dss
From Proteopedia
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==Overview== | ==Overview== | ||
| - | 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 ... | + | 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. |
==About this Structure== | ==About this Structure== | ||
| - | 1DSS is a | + | 1DSS is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Palinurus_versicolor Palinurus versicolor] with SO4 and NAD as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Glyceraldehyde-3-phosphate_dehydrogenase_(phosphorylating) Glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.1.12 1.2.1.12] Structure known Active Sites: AVG and AVR. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1DSS OCA]. |
==Reference== | ==Reference== | ||
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[[Category: molecular symmetry]] | [[Category: molecular symmetry]] | ||
| - | ''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Mon Nov 5 14:03:47 2007'' |
Revision as of 11:58, 5 November 2007
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STRUCTURE OF ACTIVE-SITE CARBOXYMETHYLATED D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE FROM PALINURUS VERSICOLOR
Overview
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.
About this Structure
1DSS is a Single protein structure of sequence from Palinurus versicolor with SO4 and NAD as ligands. Active as Glyceraldehyde-3-phosphate dehydrogenase (phosphorylating), with EC number 1.2.1.12 Structure known Active Sites: AVG and AVR. Full crystallographic information is available from OCA.
Reference
Structure of active site carboxymethylated D-glyceraldehyde-3-phosphate dehydrogenase from Palinurus versicolor., Song SY, Xu YB, Lin ZJ, Tsou CL, J Mol Biol. 1999 Apr 9;287(4):719-25. PMID:10191140
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