PDBsum entry: 1wls

Hydrolase

PDB-id: 1wls

Biological unit* = asymmetric unit,
as shown
(*as deduced by PQS)

Contents

Description

Header details

Header records

References

PROCHECK

Protein chains

328 a.a. *

Waters ×250

* Residue conservation analysis

Tools

Clefts Calculation

PDB id:

1wls

Name:

Hydrolase

Title:

Crystal structure of l-asparaginase i homologue protein from pyrococcus horikoshii

Structure:

L-asparaginase. Chain: a, b. Engineered: yes

Source:

Pyrococcus horikoshii. Organism_taxid: 53953. Gene: ph0066. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biological unit:

Dimer (from PQS)

UniProt:

Chains A, B: O57797 (O57797_PYRHO)

Seq:

Struc:

Seq:

328 a.a.

Struc:

328 a.a.

Key:	PfamA domain
Secondary structure	CATH domain

Resolution:

2.16Å

R-factor:

0.211

R-free:

0.253

Authors:

M.Yao,H.Morita,Y.Yasutake,I.Tanaka

Key ref:

M.Yao et al. (2005). Structure of the type I L-asparaginase from the hyperthermophilic archaeon Pyrococcus horikoshii at 2.16 angstroms resolution.. Acta Crystallogr D Biol Crystallogr, 61, 294-301. [PubMed id: 15735339] [DOI: 10.1107/S0907444904032950]

Date:

29-Jun-04

Release date:

15-Mar-05

Quick_links

Procheck

Clefts

Surface

Key reference

DOI no: 10.1107/S0907444904032950

Acta Crystallogr D Biol Crystallogr 61:294-301 (2005)

PubMed id: 15735339

Structure of the type I L-asparaginase from the hyperthermophilic archaeon Pyrococcus horikoshii at 2.16 angstroms resolution.

M.Yao, Y.Yasutake, H.Morita, I.Tanaka.

ABSTRACT

The crystal structure of the L-asparaginase from the hyperthermophilic archaeon Pyrococcus horikoshii (PhA) was determined by the multiwavelength anomalous diffraction (MAD) method and was refined to a resolution of 2.16 angstroms with a crystallographic R factor and free R factor of 21.1 and 25.3%, respectively. This is the first report of the three-dimensional structure of a type I L-asparaginase. These enyzmes are known as cytosolic L-asparaginases with lower affinities for substrate than the type II L-asparaginases. Although the overall fold of PhA was closely related to the structure of the well characterized type II L-asparaginase, structural differences were also detected. PhA forms a homodimer that corresponds to half the homotetramer of type II L-asparaginases. Structure comparison at the active site reveals that most catalytic residues are conserved except for two residues that recognize the amino group of the substrate. Additionally, a remarkable structural difference is found in the so-called 'active-site flexible loop'. In PhA this loop is stabilized by beta-hairpin formation and by elaborate interactions with the type-I-specific alpha-helical region derived from the other subunit forming the PhA dimer. The flexible loop of the type II enzyme is considered to serve as a mobile gate to the active site. Therefore, the loop stabilization observed in the PhA structure may cause limitation of the access of the substrate to the active site.

Selected figure(s)

Figure 4.
Figure 4 Active-site comparison between PhA and EcA-II. (a) Stereoview superimposition of the active-site residues of PhA (pink) and EcA-II (blue; PDB code 3eca ). The active-site flexible loop is also shown. (b) Stereoview representation of the interactions between the stabilized loop ( [beta] -hairpin) and the [alpha] -helix derived from the other subunit of PhA. The [beta] -hairpin and the [alpha] -helix are coloured yellow and pink, respectively. The figures were generated using the programs MOLSCRIPT (Kraulis, 1991 [Kraulis, P. J. (1991). J. Appl. Cryst. 24, 946-950.]-[bluearr.gif] ) and RASTER3D (Merritt & Bacon, 1997 [Merritt, E. A. & Bacon, D. J. (1997). Methods Enzymol. 277, 505-524.]-[bluearr.gif] ).

Figure 5.
Figure 5 Molecular-surface representation of the unliganded EcA-II (PDB code 1ihd ) and PhA. The molecular surface of both enzymes was calculated using the intimate dimer model. The active site of EcA-II is uncovered and exposed to the solvent (blue circle) owing to the flexibility of the loop region, while the active site of PhA is mostly covered with the inflexible [beta] -hairpin structure (blue dotted circle). The molecular surfaces were generated with the program GRASP (Nicholls et al., 1991 [Nicholls, A., Sharp, K. A. & Honig, B. (1991). Proteins Struct. Funct. Genet. 11, 281-296.]-[bluearr.gif] ).

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2005, 61, 294-301) copyright 2005.

Figures were selected by an automated process.