2ZKM | pdb_00002zkm

Crystal Structure of Phospholipase C Beta 2

• PDB DOI: https://doi.org/10.2210/pdb2ZKM/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2008-03-26 Released: 2008-08-12 
• Deposition Author(s): Hicks, S.N., Jezyk, M.R., Gershberg, S., Seifert, J.P., Harden, T.K., Sondek, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free: 
  0.213 (Depositor), 0.212 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Model: experimental

Literature

General and versatile autoinhibition of PLC isozymes

Hicks, S.N., Jezyk, M.R., Gershburg, S., Seifert, J.P., Harden, T.K., Sondek, J.

(2008) Mol Cell 31: 383-394

• PubMed: 18691970 
• DOI: https://doi.org/10.1016/j.molcel.2008.06.018
• Primary Citation Related Structures: 
  2ZKM


• PubMed Abstract: 
  

  Phospholipase C (PLC) isozymes are directly activated by heterotrimeric G proteins and Ras-like GTPases to hydrolyze phosphatidylinositol 4,5-bisphosphate into the second messengers diacylglycerol and inositol 1,4,5-trisphosphate. Although PLCs play central roles in myriad signaling cascades, the molecular details of their activation remain poorly understood. As described here, the crystal structure of PLC-beta2 illustrates occlusion of the active site by a loop separating the two halves of the catalytic TIM barrel. Removal of this insertion constitutively activates PLC-beta2 without ablating its capacity to be further stimulated by classical G protein modulators. Similar regulation occurs in other PLC members, and a general mechanism of interfacial activation at membranes is presented that provides a unifying framework for PLC activation by diverse stimuli.

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Organizational Affiliation: 
• Department of Pharmacology, The University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 91.07 kDa 
• Atom Count: 6,397 
• Modeled Residue Count: 708 
• Deposited Residue Count: 799 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase beta-2	A [auth X]	799	Homo sapiens	Mutation(s): 0  Gene Names: PLC beta 2 EC: 3.1.4.11
UniProt & NIH Common Fund Data Resources
Find proteins for Q00722 (Homo sapiens) Explore Q00722  Go to UniProtKB:  Q00722
PHAROS:  Q00722 GTEx:  ENSG00000137841

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	B [auth X]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free:  0.213 (Depositor), 0.212 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.404	α = 90
b = 86.379	β = 90
c = 147.447	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-08-12 
Deposition Author(s): Hicks, S.N., Jezyk, M.R., Gershberg, S., Seifert, J.P., Harden, T.K., Sondek, J.

Revision History  

• Version 1.0: 2008-08-12
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-11
  Changes: Refinement description
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description