2dxl: Difference between revisions
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|PDB= 2dxl |SIZE=350|CAPTION= <scene name='initialview01'>2dxl</scene>, resolution 3.00Å | |PDB= 2dxl |SIZE=350|CAPTION= <scene name='initialview01'>2dxl</scene>, resolution 3.00Å | ||
|SITE= | |SITE= | ||
|LIGAND= <scene name='pdbligand=CO:COBALT (II) ION'>CO</scene> | |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] | |ACTIVITY= <span class='plainlinks'>[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] </span> | ||
|GENE= GpdQ ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=548 Enterobacter aerogenes]) | |GENE= GpdQ ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=548 Enterobacter aerogenes]) | ||
|DOMAIN= | |||
|RELATEDENTRY=[[2dxn|2DXN]] | |||
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2dxl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dxl OCA], [http://www.ebi.ac.uk/pdbsum/2dxl PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2dxl RCSB]</span> | |||
}} | }} | ||
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[[Category: Jackson, C J.]] | [[Category: Jackson, C J.]] | ||
[[Category: Ollis, D L.]] | [[Category: Ollis, D L.]] | ||
[[Category: alpha/beta sandwich]] | [[Category: alpha/beta sandwich]] | ||
[[Category: beta-sheet extension]] | [[Category: beta-sheet extension]] | ||
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[[Category: metalloenzyme]] | [[Category: metalloenzyme]] | ||
''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 02:40:59 2008'' | ||
Revision as of 02:40, 31 March 2008
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| , resolution 3.00Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | |||||||
| Gene: | GpdQ (Enterobacter aerogenes) | ||||||
| Activity: | Glycerophosphodiester phosphodiesterase, with EC number 3.1.4.46 | ||||||
| Related: | 2DXN
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| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| 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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