3ELO | pdb_00003elo

Crystal Structure of Human Pancreatic Prophospholipase A2

• PDB DOI: https://doi.org/10.2210/pdb3ELO/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Komagataella pastoris
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2008-09-22 Released: 2009-04-14 
• Deposition Author(s): Xu, W., Yi, L., Feng, Y., Chen, L., Liu, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.183 (Depositor), 0.198 (DCC) 
• R-Value Work: 
  0.145 (Depositor), 0.158 (DCC) 
• R-Value Observed: 
  0.147 (Depositor) 

Literature

Structural insight into the activation mechanism of human pancreatic prophospholipase A2

Xu, W., Yi, L., Feng, Y., Chen, L., Liu, J.

(2009) J Biological Chem 284: 16659-16666

• PubMed: 19297324 
• DOI: https://doi.org/10.1074/jbc.M808029200
• Primary Citation Related Structures: 
  3ELO


• PubMed Abstract: 
  

  Pancreatic phospholipase A2 (phospholipase A2 group 1B, G1B) belongs to the superfamily of secreted phospholipase A2 (PLA2) enzymes. G1B has been proposed to be a potential target for diseases such as hypertension, obesity, and diabetes. Human pancreatic prophospholipase A2 (pro-hG1B) is activated by cleavage of the first seven-residue propeptide (phospholipase A2 propeptide, PROP). However, questions still remain on the mode of action for pro-hG1B. In this work, we expressed pro-hG1B in Pichia pastoris and determined the crystal structure at 1.55-A resolution. The x-ray structure demonstrates that pro-hG1B forms a trimer. In addition, PROP occupies the catalytic cavity and can be self-cleaved at 37 degrees C. A new membrane-bound surface and activation mechanism are proposed based on the trimeric model of pro-hG1B. We also propose a new autoproteolytic mechanism for pro-hG1B by the reaction triad Asp49-Arg0-Ser(-2) that is similar to the serine protease catalytic triad.

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Organizational Affiliation: 
• From the Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510663, China; Graduate University of Chinese Academy of Sciences, Beijing 100049, China.
From the Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510663, China.
From the Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510663, China; School of Life Sciences, University of Science and Technology of China, Hefei 230027, China. Electronic address: [e-mail].
From the Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510663, China; School of Life Sciences, University of Science and Technology of China, Hefei 230027, China. Electronic address: [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 14.97 kDa 
• Atom Count: 1,223 
• Modeled Residue Count: 133 
• Deposited Residue Count: 133 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phospholipase A2	A	133	Homo sapiens	Mutation(s): 0  Gene Names: PLA2G1B EC: 3.1.1.4 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P04054 (Homo sapiens) Explore P04054  Go to UniProtKB:  P04054
PHAROS:  P04054 GTEx:  ENSG00000170890

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.183 (Depositor), 0.198 (DCC) 
• R-Value Work:  0.145 (Depositor), 0.158 (DCC) 
• R-Value Observed: 0.147 (Depositor) 

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.549	α = 90
b = 56.549	β = 90
c = 60.631	γ = 120

Software Package:

Software Name	Purpose
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrysalisPro	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-04-14 
Deposition Author(s): Xu, W., Yi, L., Feng, Y., Chen, L., Liu, J.

Revision History  

• Version 1.0: 2009-04-14
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2014-02-05
  Changes: Database references
• Version 1.3: 2024-11-13
  Changes: Data collection, Database references, Derived calculations, Structure summary