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PDBsum entry 2dxl
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References listed in PDB file
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Key reference
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Title
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The structure and function of a novel glycerophosphodiesterase from enterobacter aerogenes.
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Authors
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C.J.Jackson,
P.D.Carr,
J.W.Liu,
S.J.Watt,
J.L.Beck,
D.L.Ollis.
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Ref.
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J Mol Biol, 2007,
367,
1047-1062.
[DOI no: ]
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PubMed id
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Abstract
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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.
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Figure 1.
Figure 1. The hydrolysis of the glycerophosphodiester
sn-glycero-3-phosphoethanolamine. The leaving group will be
protonated at physiological pH.
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Figure 2.
Figure 2. (Top) A topology diagram of GpdQ, illustrating the
catalytic α/β sandwich domain (β1–β7/αA–αF; 1–196),
the all β-strand dimerisation domain (β8–β12; 197–256),
and the domain swapped cap domain (β13, αG; 257–271) that is
stabilised by an inter-chain disulfide bond. The locations of
the liganding residues are shown. (Below) A ribbon diagram and
carbon-α trace (red) of dimeric GpdQ, showing the location of
the active site metals at the center of the α/β sandwich
domain and the disulfide bond (yellow).
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2007,
367,
1047-1062)
copyright 2007.
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Secondary reference #1
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Title
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The purification, Crystallization and preliminary diffraction of a glycerophosphodiesterase from enterobacter aerogenes.
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Authors
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C.J.Jackson,
P.D.Carr,
H.K.Kim,
J.W.Liu,
D.L.Ollis.
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Ref.
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Acta Crystallogr Sect F Struct Biol Cryst Commun, 2006,
62,
659-661.
[DOI no: ]
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PubMed id
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Figure 2.
Needles of GpdQ in 1.9 M sodium malonate pH 7.0. The scale is
0.025 mm per gradation. Acta Crystallogr Sect F Struct Biol
Cryst Commun. 2006 July 1; 62(Pt 7): 659–661. Published online
2006 June 10. doi: 10.1107/S1744309106020021. Copyright
[copyright] International Union of Crystallography 2006
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Figure 3.
Crystals of apo-GpdQ in 1.9 M sodium malonate pH 7.0. The
scale is 0.025 mm per gradation. Acta Crystallogr Sect F Struct
Biol Cryst Commun. 2006 July 1; 62(Pt 7): 659–661. Published
online 2006 June 10. doi: 10.1107/S1744309106020021. Copyright
[copyright] International Union of Crystallography 2006
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The above figures are
reproduced from the cited reference
which is an Open Access publication published by the IUCr
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