Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 35.09 kDa 
• Atom Count: 2761 
• Modelled Residue Count: 306 
• Deposited Residue Count: 306 
• Unique protein chains: 1

3V1H

Structure of the H258Y mutant of Phosphatidylinositol-specific phospholipase C from Staphylococcus aureus

• PDB DOI: 10.2210/pdb3V1H/pdb

• Classification: LYASE
• Organism(s): Staphylococcus aureus subsp. aureus str. Newman
• Mutation(s): Yes 


• Deposited: 2011-12-09 Released: 2012-04-04 
• Deposition Author(s): Goldstein, R.I., Cheng, J., Stec, B., Roberts, M.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.237 
• R-Value Work: 0.187 
• R-Value Observed: 0.189 

Literature

Structure of the S. aureus PI-Specific Phospholipase C Reveals Modulation of Active Site Access by a Titratable PI-Cation Latched Loop

Goldstein, R., Cheng, J., Stec, B., Roberts, M.F.

(2012) Biochemistry 51: 2579-2587

• PubMed: 22390775 
• DOI: 10.1021/bi300057q
• Primary Citation of Related Structures:  
  3V16, 3V18, 3V1H


• PubMed Abstract: 
  

Staphylococcus aureus secretes a phosphatidylinositol-specific phospholipase C (PI-PLC) as a virulence factor that is unusual in exhibiting higher activity at acidic pH values than other enzymes in this class. We have determined the crystal structure of this enzyme at pH 4.6 and pH 7.5. Under slightly basic conditions, the S. aureus PI-PLC structure closely follows the conformation of other bacterial PI-PLCs. However, when crystallized under acidic conditions, a large section of mobile loop at the αβ-barrel rim in the vicinity of the active site shows ~10 Å shift. This loop displacement at acidic pH is the result of a titratable intramolecular π-cation interaction between His258 and Phe249. This was verified by a structure of the mutant protein H258Y crystallized at pH 4.6, which does not exhibit the large loop shift. The intramolecular π-cation interaction for S. aureus PI-PLC provides an explanation for the activity of the enzyme at acid pH and also suggests how phosphatidylcholine, as a competitor for Phe249, may kinetically activate this enzyme.

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Organizational Affiliation: 

Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
1-phosphatidylinositol phosphodiesterase	A	306	Staphylococcus aureus subsp. aureus str. Newman	Mutation(s): 1  Gene Names: plc, NWMN_0041 EC: 4.6.1.13
UniProt
Find proteins for P45723 (Staphylococcus aureus (strain Newman)) Explore P45723  Go to UniProtKB:  P45723

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
INS	B [auth A]	1,2,3,4,5,6-HEXAHYDROXY-CYCLOHEXANE C6 H12 O6 CDAISMWEOUEBRE-GPIVLXJGSA-N
ACT	C [auth A], D [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.237 
• R-Value Work: 0.187 
• R-Value Observed: 0.189 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.95	α = 90
b = 57.215	β = 90
c = 61.144	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHASER	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
HKL-2000	data collection

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-12-09 
• Released Date: 2012-04-04 
Deposition Author(s): Goldstein, R.I., Cheng, J., Stec, B., Roberts, M.F.

Revision History  

• Version 1.0: 2012-04-04
  Type: Initial release
  
• Version 1.1: 2012-04-18
  Changes: Other
• Version 1.2: 2019-07-17
  Changes: Data collection, Refinement description