PDBsum entry 1isp

Hydrolase

PDB id: 1isp

Contents

Protein chain

179 a.a. *

Ligands

GOL

Waters ×151

* Residue conservation analysis

PDB id:

1isp

Name:

Hydrolase

Title:

Crystal structure of bacillus subtilis lipase at 1.3a resolution

Structure:

Lipase. Chain: a. Engineered: yes

Source:

Bacillus subtilis. Organism_taxid: 1423. Gene: lipa. Expressed in: bacillus megaterium. Expression_system_taxid: 1404.

Resolution:

1.30Å R-factor: 0.192 R-free: 0.232

Authors:

K.Kawasaki,H.Kondo,M.Suzuki,S.Ohgiya,S.Tsuda

Key ref:

K.Kawasaki et al. (2002). Alternate conformations observed in catalytic serine of Bacillus subtilis lipase determined at 1.3 A resolution. Acta Crystallogr D Biol Crystallogr, 58, 1168-1174. PubMed id: 12077437 DOI: 10.1107/S090744490200714X

Date:

19-Dec-01 Release date: 19-Dec-02

Protein chain

P37957  (ESTA_BACSU) -  Lipase EstA from Bacillus subtilis (strain 168)

Seq: 212 a.a.

Struc: 179 a.a.

Enzyme reactions

• Enzyme class: E.C.3.1.1.3 - triacylglycerol lipase.
• Reaction: a triacylglycerol + H2O = a diacylglycerol + a fatty acid + H⁺

triacylglycerol + H2O = diacylglycerol (Bound ligand (Het Group name = GOL) matches with 50.00% similarity) + fatty acid + H(+)

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

reference

DOI no: 10.1107/S090744490200714X

Acta Crystallogr D Biol Crystallogr 58:1168-1174 (2002)

PubMed id: 12077437

Alternate conformations observed in catalytic serine of Bacillus subtilis lipase determined at 1.3 A resolution.

K.Kawasaki, H.Kondo, M.Suzuki, S.Ohgiya, S.Tsuda.

ABSTRACT

Bacillus subtilis extracellular lipase (BsL) has an exceptionally low molecular weight (19.4 kDa) for a member of the lipase family. A crystallographic study was performed on BsL in order to design and produce mutant BsL that will be more suitable for industrial uses based on analysis of the three-dimensional structure. Recently, the crystal structure of BsL has been determined at 1.5 A resolution [van Pouderoyen et al. (2001). J. Mol. Biol. 309, 215-226]. In the present study, a new crystal form of BsL which provides diffraction data to higher resolution was obtained and its structure was determined at 1.3 A using the MAD method. It was found that the active-site residue Ser77 has alternate side-chain conformations. The O(gamma) atom of the first conformer forms a hydrogen bond to the N(epsilon) atom of His155, a member of the catalytic triad. In contrast, the second conformer is constructed with a hydrogen bond to the side-chain atom of the adjacent His76. These two conformers presumably correspond to the active and inactive states, respectively. Similar alternate conformations in the catalytic serine residue have been observed in Fusarium solani cutinase determined at 1.0 A resolution and Penicillium purpurogenum acetylxylan esterase at 0.9 A resolution. In addition, a glycerol molecule, which was used as a cryoprotectant, is found to be located in the active site. On the basis of these results, a model for substrate binding in the reaction-intermediate state of BsL is proposed.

Selected figure(s)

Figure 1.
Figure 1 A schematic drawing of BsL produced with MOLSCRIPT (Kraulis, 1991[Kraulis, P. J. (1991). J. Appl. Cryst. 24, 946-950.]) and RASTER3D (Merritt & Bacon, 1997[Merritt, E. A. & Bacon, D. J. (1997). Methods. Enzymol. 277, 505-524.]). Secondary structures are labelled ( 1- 6, 1- 5). The side chains of the catalytic triad (Ser77, Asp133 and His156) are represented in ball-and-stick. The N- and C-termini are denoted N and C, respectively.

Figure 4.
Figure 4 Omit map for the glycerol molecule at the active site. [A]-weighted 2F[o] - F[c] and F[o] - F[c] maps are drawn in blue and red, respectively. Each map is contoured at 2 . One hydroxyl O atom of the glycerol is labelled O1.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2002, 58, 1168-1174) copyright 2002.

Figures were selected by an automated process.