PDBsum entry 2bd1

Hydrolase

PDB id: 2bd1

Contents

Protein chains

123 a.a. *

Ligands

MPD ×2

Metals

_CA ×4

Waters ×218

* Residue conservation analysis

PDB id:

2bd1

Name:

Hydrolase

Title:

A possible role of the second calcium ion in interfacial binding: atomic and medium resolution crystal structures of the quadruple mutant of phospholipase a2

Structure:

Phospholipase a2. Chain: a, b. Synonym: phosphatidylcholine 2-acylhydrolase, group ib phospholipase a2. Engineered: yes. Mutation: yes

Source:

Bos taurus. Cattle. Organism_taxid: 9913. Gene: pla2g1b. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.90Å R-factor: 0.207 R-free: 0.240

Authors:

K.Sekar,D.Velmurugan,M.D.Tsai

Key ref:

K.Sekar et al. (2006). Suggestive evidence for the involvement of the second calcium and surface loop in interfacial binding: monoclinic and trigonal crystal structures of a quadruple mutant of phospholipase A2. Acta Crystallogr D Biol Crystallogr, 62, 717-724. PubMed id: 16790927 DOI: 10.1107/S0907444906014855

Date:

19-Oct-05 Release date: 04-Jul-06

Protein chains

P00593  (PA21B_BOVIN) -  Phospholipase A2 from Bos taurus

Seq: 145 a.a.

Struc: 123 a.a.*

* PDB and UniProt seqs differ at 4 residue positions (black crosses)

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/S0907444906014855

Acta Crystallogr D Biol Crystallogr 62:717-724 (2006)

PubMed id: 16790927

Suggestive evidence for the involvement of the second calcium and surface loop in interfacial binding: monoclinic and trigonal crystal structures of a quadruple mutant of phospholipase A2.

K.Sekar, M.Yogavel, S.P.Kanaujia, A.Sharma, D.Velmurugan, M.J.Poi, Z.Dauter, M.D.Tsai.

ABSTRACT

The crystal structures of the monoclinic and trigonal forms of the quadruple mutant K53,56,120,121M of recombinant bovine pancreatic phospholipase A2 (PLA2) have been solved and refined at 1.9 and 1.1 A resolution, respectively. Interestingly, the monoclinic form reveals the presence of the second calcium ion. Furthermore, the surface-loop residues are ordered and the conformation of residues 62-66 is similar to that observed in other structures containing the second calcium ion. On the other hand, in the trigonal form the surface loop is disordered and the second calcium is absent. Docking studies suggest that the second calcium and residues Lys62 and Asp66 from the surface loop could be involved in the interaction with the polar head group of the membrane phospholipid. It is hypothesized that the two structures of the quadruple mutant, monoclinic and trigonal, represent the conformations of PLA2 at the lipid interface and in solution, respectively. A docked structure with a phospholipid molecule and with a transition-state analogue bound, one at the active site coordinating to the catalytic calcium and the other at the second calcium site, but both at the i-face, is presented.

Selected figure(s)

Figure 1.
Figure 1 The tertiary structure of the monoclinic form of the quadruple mutant of recombinant PLA[2]showing the primary (P) and the secondary (S) calcium ions. The figure was produced using the program MOLSCRIPT (Kraulis, 1991[Kraulis, P. J. (1991). J. Appl. Cryst. 24, 946-950.]). For clarity, only molecule A is shown here.

Figure 5.
Figure 5 Ensemble of conformations (99) having minimum docking energy in the most populated cluster (40%).

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2006, 62, 717-724) copyright 2006.

Figures were selected by an automated process.