2dxl: Difference between revisions
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[[Image:2dxl.gif|left|200px]] | [[Image:2dxl.gif|left|200px]] | ||
'''Glycerophosphodiesterase from Enterobacter aerogenes''' | {{Structure | ||
|PDB= 2dxl |SIZE=350|CAPTION= <scene name='initialview01'>2dxl</scene>, resolution 3.00Å | |||
|SITE= | |||
|LIGAND= <scene name='pdbligand=CO:COBALT (II) ION'>CO</scene> | |||
|ACTIVITY= [http://en.wikipedia.org/wiki/Glycerophosphodiester_phosphodiesterase Glycerophosphodiester phosphodiesterase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.4.46 3.1.4.46] | |||
|GENE= GpdQ ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=548 Enterobacter aerogenes]) | |||
}} | |||
'''Glycerophosphodiesterase from Enterobacter aerogenes''' | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
2DXL is a [ | 2DXL is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Enterobacter_aerogenes Enterobacter aerogenes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DXL OCA]. | ||
==Reference== | ==Reference== | ||
The structure and function of a novel glycerophosphodiesterase from Enterobacter aerogenes., Jackson CJ, Carr PD, Liu JW, Watt SJ, Beck JL, Ollis DL, J Mol Biol. 2007 Apr 6;367(4):1047-62. Epub 2007 Jan 20. PMID:[http:// | The structure and function of a novel glycerophosphodiesterase from Enterobacter aerogenes., Jackson CJ, Carr PD, Liu JW, Watt SJ, Beck JL, Ollis DL, J Mol Biol. 2007 Apr 6;367(4):1047-62. Epub 2007 Jan 20. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17306828 17306828] | ||
[[Category: Enterobacter aerogenes]] | [[Category: Enterobacter aerogenes]] | ||
[[Category: Glycerophosphodiester phosphodiesterase]] | [[Category: Glycerophosphodiester phosphodiesterase]] | ||
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[[Category: metalloenzyme]] | [[Category: metalloenzyme]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 16:32:54 2008'' | ||
Revision as of 17:32, 20 March 2008
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| , resolution 3.00Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | |||||||
| Gene: | GpdQ (Enterobacter aerogenes) | ||||||
| Activity: | Glycerophosphodiester phosphodiesterase, with EC number 3.1.4.46 | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Glycerophosphodiesterase from Enterobacter aerogenes
OverviewOverview
The structure of the glycerophosphodiesterase (GDPD) from Enterobacter aerogenes, GpdQ, has been solved by SAD phasing from the active site metal ions. Structural analysis indicates that GpdQ belongs to the alpha/beta sandwich metallo-phosphoesterase family, rather than the (alpha/beta)(8) barrel GDPD family, suggesting that GpdQ is a structurally novel GDPD. Hexameric GpdQ is generated by interactions between three dimers. The dimers are formed through domain swapping, stabilised by an inter-chain disulfide bond, and beta-sheet extension. The active site contains a binuclear metal centre, with a fully occupied alpha-metal ion site, and partially occupied beta-metal ion site, as revealed by anomalous scattering analysis. Using a combination of TLS refinement and normal mode analysis, the dynamic movement of GpdQ was investigated. This analysis suggests that the hexameric quaternary structure stabilises the base of the dimer, which promotes "breathing" of the active site cleft. Comparison with other metallo-phosphodiesterases shows that although the central, catalytic, domain is highly conserved, many of these enzymes possess structurally unrelated secondary domains located at the entrance of the active site. We suggest that this could be a common structural feature of metallo-phosphodiesterases that constrains substrate specificity, preventing non-specific phosphodiester hydrolysis.
About this StructureAbout this Structure
2DXL is a Single protein structure of sequence from Enterobacter aerogenes. Full crystallographic information is available from OCA.
ReferenceReference
The structure and function of a novel glycerophosphodiesterase from Enterobacter aerogenes., Jackson CJ, Carr PD, Liu JW, Watt SJ, Beck JL, Ollis DL, J Mol Biol. 2007 Apr 6;367(4):1047-62. Epub 2007 Jan 20. PMID:17306828
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