2gqa: Difference between revisions
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'''Structure of NADH-reduced SYE1, an OYE homologue from S. oneidensis''' | '''Structure of NADH-reduced SYE1, an OYE homologue from S. oneidensis''' | ||
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[[Category: Hemel, D van den.]] | [[Category: Hemel, D van den.]] | ||
[[Category: Savvides, S N.]] | [[Category: Savvides, S N.]] | ||
[[Category: | [[Category: Flavoenzyme]] | ||
[[Category: | [[Category: Fmn]] | ||
[[Category: | [[Category: Old yellow enzyme]] | ||
[[Category: | [[Category: Reduction by nadh]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 05:23:55 2008'' | |||
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Revision as of 05:23, 4 May 2008
Structure of NADH-reduced SYE1, an OYE homologue from S. oneidensis
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
2GQA is a Single protein structure of sequence from Shewanella oneidensis. 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 Page seeded by OCA on Sun May 4 05:23:55 2008