1ihx
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(New page: 200px<br /><applet load="1ihx" size="450" color="white" frame="true" align="right" spinBox="true" caption="1ihx, resolution 2.80Å" /> '''Crystal structure of...)
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Revision as of 15:17, 20 November 2007
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Crystal structure of two D-glyceraldehyde-3-phosphate dehydrogenase complexes: a case of asymmetry
Overview
Crystal structures of GAPDH from Palinurus versicolor complexed with two, coenzyme analogues, SNAD(+) and ADP-ribose, were determined by molecular, replacement and refined at medium resolution to acceptable, crystallographic factors and reasonable stereochemistry. ADP-ribose in the, ADP-ribose-GAPDH complex adopts a rather extended conformation. The, interactions between ADP-ribose and GAPDH are extensive and in a fashion, dissimilar to the coenzyme NAD(+). This accounts for the strong inhibiting, ability of ADP-ribose. The conformational changes induced by ADP-ribose, binding are quite different to those induced by NAD(+) binding. This, presumably explains the non-cooperative behaviour of the ADP-ribose, binding. Unexpectedly, the SNAD(+)-GAPDH complex reveals pairwise, asymmetry. The asymmetry is significant, including the SNAD(+) molecule, active-site structure and domain motion induced by the coenzyme analogue., In the yellow or red subunits [nomenclature of subunits is as in Buehner, et al. (1974). J. Mol. Biol. 90, 25-49], SNAD(+) binds similarly, as does, NAD(+) in holo-GAPDH. While, in the green or blue subunit, the SNAD(+), binds in a non-productive manner, resulting in a disordered, thionicotinamide ring and rearranged active-site residues. The, conformation seen in the yellow and red subunits of SNAD(+)-GAPDH is, likely to represent the functional state of the enzyme complex in solution, and thus accounts for the substrate activity of SNAD(+). A novel type of, domain motion is observed for the binding of the coenzyme analogues to, GAPDH. The possible conformational transitions involved in the coenzyme, binding and the important role of the nicotinamide group are discussed.
About this Structure
1IHX is a Single protein structure of sequence from Palinurus versicolor with SO4 and SND as ligands. Active as Glyceraldehyde-3-phosphate dehydrogenase (phosphorylating), with EC number 1.2.1.12 Full crystallographic information is available from OCA.
Reference
Structures of D-glyceraldehyde-3-phosphate dehydrogenase complexed with coenzyme analogues., Shen YQ, Song SY, Lin ZJ, Acta Crystallogr D Biol Crystallogr. 2002 Aug;58(Pt 8):1287-97. Epub 2002, Jul 20. PMID:12136140
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