PDBsum entry 2wt4

Hydrolase

PDB id: 2wt4

Contents

Protein chain

315 a.a.

Ligands

ASP

Waters ×168

References listed in PDB file

Key reference

Title

Structure of helicobacter pyloril-Asparaginase at 1.4 a resolution.

Authors

P.Dhavala, A.C.Papageorgiou.

Ref.

Acta Crystallogr D Biol Crystallogr, 2009, 65, 1253-1261. [DOI no: 10.1107/S0907444909038244]

PubMed id

19966411

Abstract

Bacterial L-asparaginases have been used in the treatment of childhood acute lymphoblastic leukaemia for over 30 years. Their therapeutic effect is based on their ability to catalyze the conversion of L-asparagine, an essential amino acid in certain tumours, to L-aspartic acid and ammonia. Two L-asparaginases, one from Escherichia coli and the other from Erwinia chrysanthemi, have been widely employed in clinical practice as anti-leukaemia drugs. However, L-asparaginases are also able to cause severe side effects owing to their intrinsic glutaminase activity. Helicobacter pylori L-asparaginase (HpA) has been reported to have negligible glutaminase activity. To gain insight into the properties of HpA, its crystal structure in the presence of L-aspartate was determined to 1.4 A resolution, which is one of the highest resolutions obtained for an L-asparaginase structure. The final structure has an R(cryst) of 12.6% (R(free) = 16.9%) with good stereochemistry. A detailed analysis of the active site showed major differences in the active-site flexible loop and in the 286-297 loop from the second subunit, which is involved in active-site formation. Accordingly, Glu289, Asn255 and Gln63 are suggested to play roles in modulating the accessibility of the active site. Overall, the structural comparison revealed that HpA has greater structural similarity to E. coli L-asparaginase than to any other L-asparaginase, including Er. carotovora L-asparaginase, despite the fact that the latter is also characterized by low glutaminase activity.

Figure 1.
Figure 1 (a) Cartoon diagram of HpA. The colouring scheme is from blue (N-terminus) to red (C-terminus). The active-site location is indicated by the bound L-Asp (shown in stick representation). Secondary-structure elements were assigned with DSSP (Kabsch & Sander, 1983[Kabsch, W. & Sander, C. (1983). Biopolymers, 22, 2577-2637.]). (b) Cartoon representation of the HpA tetramer. Each monomer is shown in a different colour. The orientation of the blue-coloured monomer is the same as in (a). The blue-salmon and green-magenta pairs correspond to intimate dimers. L-Asp is depicted as a space-filling model. The same structure after a 90° rotation is shown on the right. This figure was created with PyMOL v.0.99 (DeLano Scientific, Palo Alto, California, USA).

Figure 3.
Figure 3 Close-up stereodiagram of the active-site flexible loop. Residues are shown in stick representation. HpA, EwA and EcAII are coloured blue, green and magenta, respectively. L-Asp is labelled.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2009, 65, 1253-1261) copyright 2009.