PDBsum entry 1kvx

Hydrolase

PDB id: 1kvx

Contents

Protein chain

123 a.a. *

Metals

_CA

Waters ×98

* Residue conservation analysis

PDB id:

1kvx

Name:

Hydrolase

Title:

Carboxylic ester hydrolase, single mutant d99a of bovine pancreatic pla2, 1.9 a orthorhombic form

Structure:

Phospholipase a2. Chain: a. Engineered: yes. Mutation: yes

Source:

Bos taurus. Cattle. Organism_taxid: 9913. Cell_line: bl21. Organ: pancreas. Gene: mature pla2. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.90Å R-factor: 0.200 R-free: 0.313

Authors:

M.Sundaralingam

Key ref:

K.Sekar et al. (1999). Structures of the catalytic site mutants D99A and H48Q and the calcium-loop mutant D49E of phospholipase A2. Acta Crystallogr D Biol Crystallogr, 55, 443-447. PubMed id: 10089353 DOI: 10.1107/S0907444998013699

Date:

28-Apr-98 Release date: 18-Nov-98

Protein chain

P00593  (PA21B_BOVIN) -  Phospholipase A2 from Bos taurus

Seq: 145 a.a.

Struc: 123 a.a.*

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

Enzyme reactions

• Enzyme class: E.C.3.1.1.4 - phospholipase A2.
• Reaction: a 1,2-diacyl-sn-glycero-3-phosphocholine + H2O = a 1-acyl-sn-glycero-3- phosphocholine + a fatty acid + H⁺
• Cofactor: Ca(2+)

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

reference

DOI no: 10.1107/S0907444998013699

Acta Crystallogr D Biol Crystallogr 55:443-447 (1999)

PubMed id: 10089353

Structures of the catalytic site mutants D99A and H48Q and the calcium-loop mutant D49E of phospholipase A2.

K.Sekar, R.Biswas, Y.Li, M.Tsai, M.Sundaralingam.

ABSTRACT

Crystal structures of the active-site mutants D99A and H48Q and the calcium-loop mutant D49E of bovine phospholipase A2 have been determined at around 1.9 A resolution. The D99A mutant is isomorphous to the orthorhombic recombinant enzyme, space group P212121. The H48Q and the calcium-loop mutant D49E are isomorphous to the trigonal recombinant enzyme, space group P3121. The two active-site mutants show no major structural perturbations. The structural water is absent in D99A and, therefore, the hydrogen-bonding scheme is changed. In H48Q, the catalytic water is present and hydrogen bonded to Gln48 N, but the second water found in native His48 is absent. In the calcium-loop mutant D49E, the two water molecules forming the pentagonal bipyramid around calcium are absent and only one O atom of the Glu49 carboxylate group is coordinated to calcium, resulting in only four ligands.

Selected figure(s)

Figure 3.
Figure 3 The same stereoview of the calcium coordination in (a) the mutant D49E and (b) in the trigonal recombinant PLA2 (Sekar et al., 1998[Sekar, K., Sekharudu, Y. C., Tsai, M.-D. & Sundaralingam, M. (1998). Acta Cryst. D54, 342-346.]). The calcium ion is shown as a solid circle. The equatorial calcium water W5 and the axial calcium water W12 are missing in the mutant and are shown as open circles. In the mutant, only one of the carboxylate O atoms is liganded to calcium, compared with the recombinant enzyme where Asp49 forms a bidentate ligation. Thus, calcium has only four ligands in the mutant while it has seven ligands in the recombinant enzyme.

Figure 4.
Figure 4 The omit electron density of the mutated residue Glu49 and the calcium ion. Contours are shown at the 1.0 level. Note that there are only four ligands around the calcium ion.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (1999, 55, 443-447) copyright 1999.

Figures were selected by an automated process.