PDBsum entry 2plq

Hydrolase

PDB id: 2plq

Contents

Protein chain

340 a.a. *

Waters ×305

* Residue conservation analysis

PDB id:

2plq

Name:

Hydrolase

Title:

Crystal structure of the amidase from geobacillus pallidus rapc8

Structure:

Aliphatic amidase. Chain: a. Synonym: acylamide amidohydrolase. Engineered: yes

Source:

Geobacillus pallidus. Organism_taxid: 33936. Strain: rapc8. Gene: amie, ami. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

1.90Å R-factor: 0.147 R-free: 0.177

Authors:

S.W.Kimani,B.T.Sewell,V.B.Agarkar,M.F.Sayed,D.A.Cowan

Key ref:

V.B.Agarkar et al. (2006). The quaternary structure of the amidase from Geobacillus pallidus RAPc8 is revealed by its crystal packing. Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 1174-1178. PubMed id: 17142891 DOI: 10.1107/S1744309106043855

Date:

20-Apr-07 Release date: 01-May-07

Protein chain

Q9L543  (AMIE_BACSP) -  Aliphatic amidase from Bacillus sp

Seq: 348 a.a.

Struc: 340 a.a.

Enzyme reactions

• Enzyme class: E.C.3.5.1.4 - amidase.
• Reaction: a monocarboxylic acid amide + H2O = a monocarboxylate + NH4⁺

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

Added reference

DOI no: 10.1107/S1744309106043855

Acta Crystallogr Sect F Struct Biol Cryst Commun 62:1174-1178 (2006)

PubMed id: 17142891

The quaternary structure of the amidase from Geobacillus pallidus RAPc8 is revealed by its crystal packing.

V.B.Agarkar, S.W.Kimani, D.A.Cowan, M.F.Sayed, B.T.Sewell.

ABSTRACT

The amidase from Geobacillus pallidus RAPc8, a moderate thermophile, is a member of the nitrilase enzyme superfamily. It converts amides to the corresponding acids and ammonia and has application as an industrial catalyst. RAPc8 amidase has been cloned and functionally expressed in Escherichia coli and has been purified by heat treatment and a number of chromatographic steps. The enzyme was crystallized using the hanging-drop vapour-diffusion method. Crystals produced in the presence of 1.2 M sodium citrate, 400 mM NaCl, 100 mM sodium acetate pH 5.6 were selected for X-ray diffraction studies. A data set having acceptable statistics to 1.96 A resolution was collected under cryoconditions using an in-house X-ray source. The space group was determined to be primitive cubic P4(2)32, with unit-cell parameter a = 130.49 (+/-0.05) A. The structure was solved by molecular replacement using the backbone of the hypothetical protein PH0642 from Pyrococcus horikoshii (PDB code 1j31) with all non-identical side chains substituted with alanine as a probe. There is one subunit per asymmetric unit. The subunits are packed as trimers of dimers with D3 point-group symmetry around the threefold axis in such a way that the dimer interface seen in the homologues is preserved.

Selected figure(s)

Figure 2.
A crystal of the amidase from G. pallidus RAPc8. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2006 December 1; 62(Pt 12): 1174–1178. Published online 2006 November 4. doi: 10.1107/S1744309106043855. Copyright [copyright] International Union of Crystallography 2006

Figure 4.
Stereoviews of the suggested solution hexamer viewed down one of the twofold axes from both directions. The preserved dimer surface is centred in (a). The interacting surfaces depicted in the foreground of (b) are based on the model of the putative CN hydrolase from yeast (PDB code 1f89). 66 C-terminal amino acids for each subunit are not depicted in this model. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2006 December 1; 62(Pt 12): 1174–1178. Published online 2006 November 4. doi: 10.1107/S1744309106043855. Copyright [copyright] International Union of Crystallography 2006

The above figures are reprinted from an Open Access publication published by the IUCr: Acta Crystallogr Sect F Struct Biol Cryst Commun (2006, 62, 1174-1178) copyright 2006.

Figures were selected by an automated process.