4EDJ | pdb_00004edj

Crystal structure of the GRASP55 GRASP Domain with a phosphomimetic mutation (S189D)

• PDB DOI: https://doi.org/10.2210/pdb4EDJ/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2012-03-27 Released: 2012-05-09 
• Deposition Author(s): Truschel, S.T., Zhang, M., Bachert, C., Macbeth, M.R., Linstedt, A.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.271 (Depositor), 0.272 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.215 (DCC) 
• R-Value Observed: 
  0.212 (Depositor) 

Starting Model: experimental

Literature

Allosteric Regulation of GRASP Protein-dependent Golgi Membrane Tethering by Mitotic Phosphorylation.

Truschel, S.T., Zhang, M., Bachert, C., Macbeth, M.R., Linstedt, A.D.

(2012) J Biological Chem 287: 19870-19875

• PubMed: 22523075 
• DOI: https://doi.org/10.1074/jbc.M111.326256
• Primary Citation Related Structures: 
  4EDJ


• PubMed Abstract: 
  

  Mitotic phosphorylation of the conserved GRASP domain of GRASP65 disrupts its self-association, leading to a loss of Golgi membrane tethering, cisternal unlinking, and Golgi breakdown. Recently, the structural basis of the GRASP self-interaction was determined, yet the mechanism by which phosphorylation disrupts this activity is unknown. Here, we present the crystal structure of a GRASP phosphomimic containing an aspartic acid substitution for a serine residue (Ser-189) that in GRASP65 is phosphorylated by PLK1, causing a block in membrane tethering and Golgi ribbon formation. The structure revealed a conformational change in the GRASP internal ligand that prevented its insertion into the PDZ binding pocket, and gel filtration assays showed that this phosphomimic mutant exhibited a significant reduction in dimer formation. Interestingly, the structure also revealed an apparent propagation of conformational change from the site of phosphorylation to the shifted ligand, and alanine substitution of two residues (Glu-145 and Ser-146) at penultimate positions in this chain rescued dimer formation by the phosphomimic. These data reveal the structural basis of the phosphoinhibition of GRASP-mediated membrane tethering and provide a mechanism for its allosteric regulation.

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Organizational Affiliation: 
• Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 45.8 kDa 
• Atom Count: 3,471 
• Modeled Residue Count: 408 
• Deposited Residue Count: 418 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Golgi reassembly-stacking protein 2	A, B	209	Homo sapiens	Mutation(s): 1  Gene Names: GORASP2, GOLPH6
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H8Y8 (Homo sapiens) Explore Q9H8Y8  Go to UniProtKB:  Q9H8Y8
PHAROS:  Q9H8Y8 GTEx:  ENSG00000115806

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
K	C [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.271 (Depositor), 0.272 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.215 (DCC) 
• R-Value Observed: 0.212 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.857	α = 90
b = 82.547	β = 90
c = 84.059	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-05-09 
Deposition Author(s): Truschel, S.T., Zhang, M., Bachert, C., Macbeth, M.R., Linstedt, A.D.

Revision History  

• Version 1.0: 2012-05-09
  Type: Initial release
  
• Version 1.1: 2012-06-27
  Changes: Database references
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description