2gq8: Difference between revisions

{{Structure

|PDB= 2gq8 |SIZE=350|CAPTION= <scene name='initialview01'>2gq8</scene>, resolution 1.700&Aring;

|SITE=  

|LIGAND= <scene name='pdbligand=BOG:B-OCTYLGLUCOSIDE'>BOG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=AC6:P-HYDROXYACETOPHENONE'>AC6</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene> and <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene>

|GENE=  

 

'''Structure of SYE1, an OYE homologue from S. ondeidensis, in complex with p-hydroxyacetophenone'''

 

 

==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.

 

==About this Structure==

2GQ8 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Shewanella_oneidensis Shewanella oneidensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GQ8 OCA].  

 

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:[http://www.ncbi.nlm.nih.gov/pubmed/16857682 16857682]

[[Category: Shewanella oneidensis]]

[[Category: Single protein]]

[[Category: Hemel, D van den.]]

[[Category: Savvides, S N.]]

[[Category: AC6]]

[[Category: BOG]]

[[Category: FMN]]

[[Category: flavoenzyme]]

[[Category: fmn]]

[[Category: old yellow enzyme]]

[[Category: phenolic ligand]]