PDBsum entry: 2or2

Lyase

PDB id: 2or2

Contents

Protein chains

296 a.a. *

Waters ×576

* Residue conservation analysis

PDB id:

2or2

Name:

Lyase

Title:

Structure of the w47a/w242a mutant of bacterial phosphatidylinositol-specific phospholipasE C

Structure:

1-phosphatidylinositol phosphodiesterase. Chain: a, b. Synonym: phosphatidylinositol diacylglycerol-lyase, phosphatidylinositol-specific phospholipasE C, pi-plc. Engineered: yes. Mutation: yes

Source:

Bacillus thuringiensis. Organism_taxid: 1428. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

1.84Å R-factor: 0.186 R-free: 0.215

Authors:

C.Shao,X.Shi,H.Wehbi,C.Zambonelli,J.F.Head,B.A.Seaton, M.F.Roberts

Key ref:

C.Shao et al. (2007). Dimer structure of an interfacially impaired phosphatidylinositol-specific phospholipase C. J Biol Chem, 282, 9228-9235. PubMed id: 17213187 DOI: 10.1074/jbc.M610918200

Date:

01-Feb-07 Release date: 13-Feb-07

Protein chains

P08954  (PLC_BACTU) -  1-phosphatidylinositol phosphodiesterase

Seq: 329 a.a.

Struc: 296 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.4.6.1.13 - Phosphatidylinositol diacylglycerol-lyase.
• Pathway: 1-Phosphatidyl-myo-inositol Metabolism
• Reaction: 1-phosphatidyl-1D-myo-inositol = 1D-myo-inositol 1,2-cyclic phosphate + 1,2-diacyl-sn-glycerol

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

 Gene Ontology (GO) functional annotation 

• Cellular component: extracellular region (1 term)
• Biological process: lipid metabolic process (2 terms)
• Biochemical function: lyase activity (4 terms)

reference

DOI no: 10.1074/jbc.M610918200

J Biol Chem 282:9228-9235 (2007)

PubMed id: 17213187

Dimer structure of an interfacially impaired phosphatidylinositol-specific phospholipase C.

C.Shao, X.Shi, H.Wehbi, C.Zambonelli, J.F.Head, B.A.Seaton, M.F.Roberts.

ABSTRACT

The crystal structure of the W47A/W242A mutant of phosphatidylinositol-specific phospholipase C (PI-PLC) from Bacillus thuringiensis has been solved to 1.8A resolution. The W47A/W242A mutant is an interfacially challenged enzyme, and it has been proposed that one or both tryptophan side chains serve as membrane interfacial anchors (Feng, J., Wehbi, H., and Roberts, M. F. (2002) J. Biol. Chem. 277, 19867-19875). The crystal structure supports this hypothesis. Relative to the crystal structure of the closely related (97% identity) wild-type PI-PLC from Bacillus cereus, significant conformational differences occur at the membrane-binding interfacial region rather than the active site. The Trp --> Ala mutations not only remove the membrane-partitioning aromatic side chains but also perturb the conformations of the so-called helix B and rim loop regions, both of which are implicated in interfacial binding. The crystal structure also reveals a homodimer, the first such observation for a bacterial PI-PLC, with pseudo-2-fold symmetry. The symmetric dimer interface is stabilized by hydrophobic and hydrogen-bonding interactions, contributed primarily by a central swath of aromatic residues arranged in a quasiherringbone pattern. Evidence that interfacially active wild-type PI-PLC enzymes may dimerize in the presence of phosphatidylcholine vesicles is provided by fluorescence quenching of PI-PLC mutants with pyrene-labeled cysteine residues. The combined data suggest that wild-type PI-PLC can form similar homodimers, anchored to the interface by the tryptophan and neighboring membrane-partitioning residues.

Selected figure(s)

Figure 1.
FIGURE 1. Structure of the PI-PLC W47A/W242A mutant dimer from B. thuringiensis shown in divergent (wall-eyed) stereo view. A, ribbon diagram of the dimer. N and C termini are labeled; the boxed region indicates the dimer interface (shown in detail in Fig. 1B). The active site residue His^32 is shown as a stick model, and the orange arrow points to the location of the active site. Residues Ile^43-Gly^48, which form helix B in the B. cereus structure but not in the mutant structure, and the rim loop region (Ser^236-Ser^244) are indicated by cyan or blue arrows, respectively. B, aromatic residues (stick representation; the subunits to which the residues belong are indicated with A or B in parentheses) located within the hydrophobic core of the symmetric dimer interface. Lightly colored helices are the N-terminal parts of helix G from both monomers. Shown in the cyan network is the electron density from the omit map omitting Tyr^246, Tyr^247, Tyr^248, Tyr^251, and Trp^280 from both subunits and contoured at 1.2 .

Figure 4.
FIGURE 4. Possible conformation (based on the W47A/W242A dimer structure) adopted by wild-type PI-PLC at the PC membrane interface (indicated by the gray shadow). Subunits A and B are shown in green and yellow, respectively. Tyr^246 side chains are included to indicate the orientation of the molecule similar to that shown in Fig. 1B.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2007, 282, 9228-9235) copyright 2007.

Figures were selected by an automated process.