2gq9: Difference between revisions

Revision as of 18:34, 21 February 2008

Structure of SYE1, an OYE homologue from S. oneidensis, in complex with p-hydroxybenzaldehyde

OverviewOverview

We have recently reported that Shewanella oneidensis, a Gram-negative gamma-proteobacterium with a rich arsenal of redox proteins, possesses four old yellow enzyme (OYE) homologues. Here, we report a series of high resolution crystal structures for one of these OYEs, Shewanella yellow enzyme 1 (SYE1), in its oxidized form at 1.4A resolution, which binds a molecule of PEG 400 in the active site, and in its NADH-reduced and p-hydroxybenzaldehyde- and p-hydroxyacetophenone-bound forms at 1.7A resolution. Although the overall structure of SYE1 reveals a monomeric enzyme based on the alpha(8)beta(8) barrel scaffold observed for other OYEs, the active site exhibits a unique combination of features: a strongly butterfly-bent FMN cofactor both in the oxidized and NADH-reduced forms, a collapsed and narrow active site tunnel, and a novel combination of conserved residues involved in the binding of phenolic ligands. Furthermore, we identify a second p-hydroxybenzaldehyde-binding site in a hydrophobic cleft next to the entry of the active site tunnel in the capping subdomain, formed by a restructuring of Loop 3 to an "open" conformation. This constitutes the first evidence to date for the entire family of OYEs that Loop 3 may indeed play a dynamic role in ligand binding and thus provides insights into the elusive NADH complex and into substrate binding in general. Structure-based sequence alignments indicate that the novelties we observe in SYE1 are supported by conserved residues in a number of structurally uncharacterized OYEs from the beta- and gamma-proteobacteria, suggesting that SYE1 represents a new subfamily of bacterial OYEs.

About this StructureAbout this Structure

2GQ9 is a Single protein structure of sequence from Shewanella oneidensis with , and as ligands. Full crystallographic information is available from OCA.

ReferenceReference

Ligand-induced conformational changes in the capping subdomain of a bacterial old yellow enzyme homologue and conserved sequence fingerprints provide new insights into substrate binding., van den Hemel D, Brige A, Savvides SN, Van Beeumen J, J Biol Chem. 2006 Sep 22;281(38):28152-61. Epub 2006 Jul 20. PMID:16857682

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 ==Overview==
-We have recently reported that Shewanella oneidensis, a Gram-negative, gamma-proteobacterium with a rich arsenal of redox proteins, possesses, four old yellow enzyme (OYE) homologues. Here, we report a series of high, resolution crystal structures for one of these OYEs, Shewanella yellow, enzyme 1 (SYE1), in its oxidized form at 1.4A resolution, which binds a, molecule of PEG 400 in the active site, and in its NADH-reduced and, p-hydroxybenzaldehyde- and p-hydroxyacetophenone-bound forms at 1.7A, resolution. Although the overall structure of SYE1 reveals a monomeric, enzyme based on the alpha(8)beta(8) barrel scaffold observed for other, OYEs, the active site exhibits a unique combination of features: a, strongly butterfly-bent FMN cofactor both in the oxidized and NADH-reduced, forms, a collapsed and narrow active site tunnel, and a novel combination, of conserved residues involved in the binding of phenolic ligands., Furthermore, we identify a second p-hydroxybenzaldehyde-binding site in a, hydrophobic cleft next to the entry of the active site tunnel in the, capping subdomain, formed by a restructuring of Loop 3 to an "open", conformation. This constitutes the first evidence to date for the entire, family of OYEs that Loop 3 may indeed play a dynamic role in ligand, binding and thus provides insights into the elusive NADH complex and into, substrate binding in general. Structure-based sequence alignments indicate, that the novelties we observe in SYE1 are supported by conserved residues, in a number of structurally uncharacterized OYEs from the beta- and, gamma-proteobacteria, suggesting that SYE1 represents a new subfamily of, bacterial OYEs.
+We have recently reported that Shewanella oneidensis, a Gram-negative gamma-proteobacterium with a rich arsenal of redox proteins, possesses four old yellow enzyme (OYE) homologues. Here, we report a series of high resolution crystal structures for one of these OYEs, Shewanella yellow enzyme 1 (SYE1), in its oxidized form at 1.4A resolution, which binds a molecule of PEG 400 in the active site, and in its NADH-reduced and p-hydroxybenzaldehyde- and p-hydroxyacetophenone-bound forms at 1.7A resolution. Although the overall structure of SYE1 reveals a monomeric enzyme based on the alpha(8)beta(8) barrel scaffold observed for other OYEs, the active site exhibits a unique combination of features: a strongly butterfly-bent FMN cofactor both in the oxidized and NADH-reduced forms, a collapsed and narrow active site tunnel, and a novel combination of conserved residues involved in the binding of phenolic ligands. Furthermore, we identify a second p-hydroxybenzaldehyde-binding site in a hydrophobic cleft next to the entry of the active site tunnel in the capping subdomain, formed by a restructuring of Loop 3 to an "open" conformation. This constitutes the first evidence to date for the entire family of OYEs that Loop 3 may indeed play a dynamic role in ligand binding and thus provides insights into the elusive NADH complex and into substrate binding in general. Structure-based sequence alignments indicate that the novelties we observe in SYE1 are supported by conserved residues in a number of structurally uncharacterized OYEs from the beta- and gamma-proteobacteria, suggesting that SYE1 represents a new subfamily of bacterial OYEs.
 ==About this Structure==
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 [[Category: Shewanella oneidensis]]
 [[Category: Single protein]]
-[[Category: Hemel, D.van.den.]]
+[[Category: Hemel, D van den.]]
-[[Category: Savvides, S.N.]]
+[[Category: Savvides, S N.]]
 [[Category: FMN]]
 [[Category: HBA]]
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 [[Category: phenolic ligands]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jan 29 20:05:44 2008''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 17:34:12 2008''