PDBsum entry: 1t6m

Lyase

PDB id: 1t6m

Contents

Protein chains

296 a.a. *

Metals

_CA ×4

Waters ×228

* Residue conservation analysis

PDB id:

1t6m

Name:

Lyase

Title:

X-ray structure of the r70d pi-plc enzyme: insight into the role of calcium and surrounding amino acids on active site geometry and catalysis.

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. Expression_system_taxid: 562

Resolution:

2.11Å R-factor: 0.223 R-free: 0.240

Authors:

D.Apiyo,L.Zhao,M.-D.Tsai,T.L.Selby

Key ref:

D.Apiyo et al. (2005). X-ray structure of the R69D phosphatidylinositol-specific phospholipase C enzyme: insight into the role of calcium and surrounding amino acids in active site geometry and catalysis. Biochemistry, 44, 9980-9989. PubMed id: 16042375 DOI: 10.1021/bi047896v

Date:

06-May-04 Release date: 16-Aug-05

Protein chains

P08954  (PLC_BACTU) -  1-phosphatidylinositol phosphodiesterase

Seq: 329 a.a.

Struc: 296 a.a.*

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

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: 10.1021/bi047896v

Biochemistry 44:9980-9989 (2005)

PubMed id: 16042375

X-ray structure of the R69D phosphatidylinositol-specific phospholipase C enzyme: insight into the role of calcium and surrounding amino acids in active site geometry and catalysis.

D.Apiyo, L.Zhao, M.D.Tsai, T.L.Selby.

ABSTRACT

Phosphatidylinositol-specific phospholipase Cs (PLCs) are a family of phosphodiesterases that catalyze the cleavage of the P-O bond via transesterification using the internal hydroxyl group of the substrate as a nucleophile, generating the five-membered cyclic inositol phosphate as an intermediate or product. To better understand the role of calcium in the catalytic mechanism of PLCs, we have determined the X-ray crystal structure of an engineered PLC enzyme from Bacillus thuringiensis to 2.1 A resolution. The active site of this enzyme has been altered by substituting the catalytic arginine with an aspartate at position 69 (R69D). This single-amino acid substitution converted a metal-independent, low-molecular weight enzyme into a metal ion-dependent bacterial PLC with an active site architecture similar to that of the larger metal ion-dependent mammalian PLC. The Ca(2+) ion shows a distorted square planar geometry in the active site that allows for efficient substrate binding and transition state stabilization during catalysis. Additional changes in the positions of the catalytic general acid/general base (GA/GB) were also observed, indicating the interrelation of the intricate hydrogen bonding network involved in stabilizing the active site amino acids. The functional information provided by this X-ray structure now allows for a better understanding of the catalytic mechanism, including stereochemical effects and substrate interactions, which facilitates better inhibitor design and sheds light on the possibilities of understanding how protein evolution might have occurred across this enzyme family.