2esd
From Proteopedia
(New page: 200px<br /><applet load="2esd" size="450" color="white" frame="true" align="right" spinBox="true" caption="2esd, resolution 2.55Å" /> '''Crystal Structure of...) |
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| - | [[Image:2esd.gif|left|200px]]<br /><applet load="2esd" size=" | + | [[Image:2esd.gif|left|200px]]<br /><applet load="2esd" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="2esd, resolution 2.55Å" /> | caption="2esd, resolution 2.55Å" /> | ||
'''Crystal Structure of thioacylenzyme intermediate of an Nadp Dependent Aldehyde Dehydrogenase'''<br /> | '''Crystal Structure of thioacylenzyme intermediate of an Nadp Dependent Aldehyde Dehydrogenase'''<br /> | ||
==Overview== | ==Overview== | ||
| - | Crystal structures of several members of the nonphosphorylating | + | Crystal structures of several members of the nonphosphorylating CoA-independent aldehyde dehydrogenase (ALDH) family have shown that the peculiar binding mode of the cofactor to the Rossmann fold results in a conformational flexibility for the nicotinamide moiety of the cofactor. This has been hypothesized to constitute an essential feature of the catalytic mechanism because the conformation of the cofactor required for the acylation step is not appropriate for the deacylation step. In the present study, the structure of a reaction intermediate of the E268A-glyceraldehyde 3-phosphate dehydrogenase (GAPN) from Streptococcus mutans, obtained by soaking the crystals of the enzyme/NADP complex with the natural substrate, is reported. The substrate is bound covalently in the four monomers and presents the geometric characteristics expected for a thioacylenzyme intermediate. Control experiments assessed that reduction of the coenzyme has occurred within the crystal. The structure reveals that reduction of the cofactor upon acylation leads to an extensive motion of the nicotinamide moiety with a flip of the reduced pyridinium ring away from the active site without significant changes of the protein structure. This event positions the reduced nicotinamide moiety in a pocket that likely constitutes the exit door for NADPH. Arguments are provided that the structure reported here constitutes a reasonable picture of the first thioacylenzyme intermediate characterized thus far in the ALDH family and that the position of the reduced nicotinamide moiety observed in GAPN is the one suitable for the deacylation step within all of the nonphosphorylating CoA-independent ALDH family. |
==About this Structure== | ==About this Structure== | ||
| - | 2ESD is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Streptococcus_mutans Streptococcus mutans] with NAP and G3H as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Glyceraldehyde-3-phosphate_dehydrogenase_(NADP(+)) Glyceraldehyde-3-phosphate dehydrogenase (NADP(+))], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.1.9 1.2.1.9] Full crystallographic information is available from [http:// | + | 2ESD is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Streptococcus_mutans Streptococcus mutans] with <scene name='pdbligand=NAP:'>NAP</scene> and <scene name='pdbligand=G3H:'>G3H</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Glyceraldehyde-3-phosphate_dehydrogenase_(NADP(+)) Glyceraldehyde-3-phosphate dehydrogenase (NADP(+))], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.1.9 1.2.1.9] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ESD OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Single protein]] | [[Category: Single protein]] | ||
[[Category: Streptococcus mutans]] | [[Category: Streptococcus mutans]] | ||
| - | [[Category: Ambrosio, K | + | [[Category: Ambrosio, K D.]] |
[[Category: Aubry, A.]] | [[Category: Aubry, A.]] | ||
[[Category: Benedetti, E.]] | [[Category: Benedetti, E.]] | ||
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[[Category: ternary complex]] | [[Category: ternary complex]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 17:14:06 2008'' |
Revision as of 15:14, 21 February 2008
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Crystal Structure of thioacylenzyme intermediate of an Nadp Dependent Aldehyde Dehydrogenase
Overview
Crystal structures of several members of the nonphosphorylating CoA-independent aldehyde dehydrogenase (ALDH) family have shown that the peculiar binding mode of the cofactor to the Rossmann fold results in a conformational flexibility for the nicotinamide moiety of the cofactor. This has been hypothesized to constitute an essential feature of the catalytic mechanism because the conformation of the cofactor required for the acylation step is not appropriate for the deacylation step. In the present study, the structure of a reaction intermediate of the E268A-glyceraldehyde 3-phosphate dehydrogenase (GAPN) from Streptococcus mutans, obtained by soaking the crystals of the enzyme/NADP complex with the natural substrate, is reported. The substrate is bound covalently in the four monomers and presents the geometric characteristics expected for a thioacylenzyme intermediate. Control experiments assessed that reduction of the coenzyme has occurred within the crystal. The structure reveals that reduction of the cofactor upon acylation leads to an extensive motion of the nicotinamide moiety with a flip of the reduced pyridinium ring away from the active site without significant changes of the protein structure. This event positions the reduced nicotinamide moiety in a pocket that likely constitutes the exit door for NADPH. Arguments are provided that the structure reported here constitutes a reasonable picture of the first thioacylenzyme intermediate characterized thus far in the ALDH family and that the position of the reduced nicotinamide moiety observed in GAPN is the one suitable for the deacylation step within all of the nonphosphorylating CoA-independent ALDH family.
About this Structure
2ESD is a Single protein structure of sequence from Streptococcus mutans with and as ligands. Active as Glyceraldehyde-3-phosphate dehydrogenase (NADP(+)), with EC number 1.2.1.9 Full crystallographic information is available from OCA.
Reference
The first crystal structure of a thioacylenzyme intermediate in the ALDH family: new coenzyme conformation and relevance to catalysis., D'Ambrosio K, Pailot A, Talfournier F, Didierjean C, Benedetti E, Aubry A, Branlant G, Corbier C, Biochemistry. 2006 Mar 7;45(9):2978-86. PMID:16503652
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