2dxl: Difference between revisions

Revision as of 18:03, 21 February 2008

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 with as ligand. Active as Glycerophosphodiester phosphodiesterase, with EC number 3.1.4.46 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

Page seeded by OCA on Thu Feb 21 17:03:51 2008

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OCA

@@ Line 4: / Line 4: @@
 ==Overview==
-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.
+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 Structure==
@@ Line 14: / Line 14: @@
 [[Category: Glycerophosphodiester phosphodiesterase]]
 [[Category: Single protein]]
-[[Category: Carr, P.D.]]
+[[Category: Carr, P D.]]
-[[Category: Jackson, C.J.]]
+[[Category: Jackson, C J.]]
-[[Category: Ollis, D.L.]]
+[[Category: Ollis, D L.]]
 [[Category: CO]]
 [[Category: alpha/beta sandwich]]
@@ Line 24: / Line 24: @@
 [[Category: metalloenzyme]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 23 15:10:39 2008''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 17:03:51 2008''