PDBsum entry 2dxl

Hydrolase

PDB id: 2dxl

Contents

Protein chains

271 a.a. *

Metals

_CO ×4

Waters ×65

* Residue conservation analysis

PDB id:

2dxl

Name:

Hydrolase

Title:

Glycerophosphodiesterase from enterobacter aerogenes

Structure:

Phosphohydrolase. Chain: a, b. Synonym: gpdq. Engineered: yes

Source:

Enterobacter aerogenes. Organism_taxid: 548. Gene: gpdq. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

3.00Å R-factor: 0.160 R-free: 0.194

Authors:

C.J.Jackson,P.D.Carr,D.L.Ollis

Key ref:

C.J.Jackson et al. (2007). The structure and function of a novel glycerophosphodiesterase from Enterobacter aerogenes. J Mol Biol, 367, 1047-1062. PubMed id: 17306828 DOI: 10.1016/j.jmb.2007.01.032

Date:

28-Aug-06 Release date: 22-May-07

Protein chains

Q6XBH1  (GPDQ_KLEAE) -  Glycerophosphodiester phosphodiesterase GpdQ from Klebsiella aerogenes

Seq: 274 a.a.

Struc: 271 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.3.1.4.46 - glycerophosphodiester phosphodiesterase.
• Reaction: a sn-glycero-3-phosphodiester + H2O = an alcohol + sn-glycerol 3-phosphate + H⁺

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1016/j.jmb.2007.01.032

J Mol Biol 367:1047-1062 (2007)

PubMed id: 17306828

The structure and function of a novel glycerophosphodiesterase from Enterobacter aerogenes.

C.J.Jackson, P.D.Carr, J.W.Liu, S.J.Watt, J.L.Beck, D.L.Ollis.

ABSTRACT

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.

Selected figure(s)

Figure 1.
Figure 1. The hydrolysis of the glycerophosphodiester sn-glycero-3-phosphoethanolamine. The leaving group will be protonated at physiological pH.

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).

The above figures are reprinted by permission from Elsevier: J Mol Biol (2007, 367, 1047-1062) copyright 2007.

Figures were selected by an automated process.