2gqa: Difference between revisions
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|PDB= 2gqa |SIZE=350|CAPTION= <scene name='initialview01'>2gqa</scene>, resolution 1.700Å | |PDB= 2gqa |SIZE=350|CAPTION= <scene name='initialview01'>2gqa</scene>, resolution 1.700Å | ||
|SITE= | |SITE= | ||
|LIGAND= <scene name='pdbligand= | |LIGAND= <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene> | ||
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
|DOMAIN= | |||
|RELATEDENTRY=[[2gou|2GOU]], [[2gq8|2GQ8]], [[2gq9|2GQ9]] | |||
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2gqa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gqa OCA], [http://www.ebi.ac.uk/pdbsum/2gqa PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2gqa RCSB]</span> | |||
}} | }} | ||
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[[Category: Hemel, D van den.]] | [[Category: Hemel, D van den.]] | ||
[[Category: Savvides, S N.]] | [[Category: Savvides, S N.]] | ||
[[Category: flavoenzyme]] | [[Category: flavoenzyme]] | ||
[[Category: fmn]] | [[Category: fmn]] | ||
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[[Category: reduction by nadh]] | [[Category: reduction by nadh]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 03:20:02 2008'' | ||
Revision as of 03:20, 31 March 2008
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| , resolution 1.700Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , | ||||||
| Related: | 2GOU, 2GQ8, 2GQ9
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| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
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
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