8YK5 | pdb_00008yk5

Structure of glycerophosphoethanolamine ethanolaminephosphodiesterase from Streptomyces sanglieri

• PDB DOI: https://doi.org/10.2210/pdb8YK5/pdb

• Classification: HYDROLASE
• Organism(s): Streptomyces sanglieri
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-03-04 Released: 2024-04-03 
• Deposition Author(s): Murayama, K., Sugimori, D.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.210 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.183 (Depositor) 

Starting Model: in silico

Literature

Structure of a phosphodiesterase from Streptomyces sanglieri with a novel C-terminal domain.

Murayama, K., Hosaka, T., Shirouzu, M., Sugimori, D.

(2024) Biochem Biophys Res Commun 708: 149784-149784

• PubMed: 38503170 
• DOI: https://doi.org/10.1016/j.bbrc.2024.149784
• Primary Citation Related Structures: 
  8YK5


• PubMed Abstract: 
  

  A glycerophosphoethanolamine ethanolaminephosphodiesterase (GPE-EP) from Streptomyces sanglieri hydrolyzes glycerophosphoethanolamine to phosphoethanolamine and glycerol. The structure of GPE-EP was determined by the molecular replacement method using a search model generated with AlphaFold2. This structure includes the entire length of the mature protein and it is composed of an N-terminal domain and a novel C-terminal domain connected to a flexible linker. The N-terminal domain is the catalytic domain containing calcium ions at the catalytic site. Coordination bonds were observed between five amino acid residues and glycerol. Although the function of the C-terminal domain is currently unknown, inter-domain interactions between the N- and C-terminal domains may contribute to its relatively high thermostability.

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Organizational Affiliation: 
• Division of Biomedical Measurements and Diagnostics, Graduate School of Biomedical Engineering, Tohoku University, Sendai, 980-8575, Japan; Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, 230-0045, Japan. Electronic address: [e-mail].
Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, 230-0045, Japan.
Material Science Course, Faculty of Symbiotic Systems Science and Technology, Fukushima University, 1 Kanayagawa, Fukushima, 960-1296, Japan.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 147.96 kDa 
• Atom Count: 11,153 
• Modeled Residue Count: 1,325 
• Deposited Residue Count: 1,332 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
phospholipase C	A, B	666	Streptomyces sanglieri	Mutation(s): 0  Gene Names: gpe-ep EC: 3.1.4.3
UniProt
Find proteins for A0A077KPD5 (Streptomyces sanglieri) Explore A0A077KPD5  Go to UniProtKB:  A0A077KPD5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL (Subject of Investigation/LOI)	D [auth A], F [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA (Subject of Investigation/LOI)	C [auth A], E [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.210 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 143.742	α = 90
b = 179.184	β = 120.44
c = 88.45	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
HKL-2000	data reduction
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-04-03 
Deposition Author(s): Murayama, K., Sugimori, D.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-04-03
  Type: Initial release