6IYM | pdb_00006iym

Fumarylacetoacetate hydrolase (EaFAH) from psychrophilic Exiguobacterium antarcticum

• PDB DOI: https://doi.org/10.2210/pdb6IYM/pdb

• Classification: HYDROLASE
• Organism(s): Exiguobacterium antarcticum B7
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-12-17 Released: 2019-04-03 
• Deposition Author(s): Lee, J.H., Lee, C.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.269 (Depositor), 0.272 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.205 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Literature

Structural and functional analysis of a dimeric fumarylacetoacetate hydrolase (EaFAH) from psychrophilic Exiguobacterium antarcticum.

Yoo, W., Lee, C.W., Kim, B.Y., Huong Luu Le, L.T., Park, S.H., Kim, H.W., Shin, S.C., Kim, K.K., Lee, J.H., Kim, T.D.

(2019) Biochem Biophys Res Commun 509: 773-778

• PubMed: 30630595 
• DOI: https://doi.org/10.1016/j.bbrc.2018.12.183
• Primary Citation Related Structures: 
  6IYM


• PubMed Abstract: 
  

  Fumarylacetoacetate hydrolase (FAH) is essential for the degradation of aromatic amino acids as well as for the cleavage of carbon-carbon bonds in metabolites or small organic compounds. Here, the X-ray crystal structure of EaFAH, a dimeric fumarylacetoacetate hydrolase from Exiguobacterium antarcticum, was determined, and its functional properties were investigated using biochemical methods. EaFAH adopts a mixed β-sandwich roll fold with a highly flexible lid region (Val ⁷³ -Leu ⁹⁴ ), and an Mg ²⁺ ion is bound at the active site by coordinating to the three carboxylate oxygen atoms of Glu ¹²⁴ , Glu ¹²⁶ , and Asp ¹⁵⁵ . The hydrolytic activity of EaFAH toward various substrates, including linalyl acetate was investigated using native polyacrylamide gel electrophoresis, activity staining, gel filtration, circular dichroism spectroscopy, fluorescence, and enzyme assays.

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Organizational Affiliation: 
• Department of Chemistry, College of Natural Science, Sookmyung Women's University, Seoul, 04310, South Korea; Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon, 440-746, South Korea.
Unit of Polar Genomics, Korea Polar Research Institute (KOPRI), Incheon, 21990, South Korea; Department of Polar Sciences, University of Science and Technology (UST), Incheon, 21990, South Korea.
Department of Chemistry, College of Natural Science, Sookmyung Women's University, Seoul, 04310, South Korea.
Unit of Polar Genomics, Korea Polar Research Institute (KOPRI), Incheon, 21990, South Korea.
Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon, 440-746, South Korea.
Unit of Polar Genomics, Korea Polar Research Institute (KOPRI), Incheon, 21990, South Korea; Department of Polar Sciences, University of Science and Technology (UST), Incheon, 21990, South Korea. Electronic address: [e-mail].
Department of Chemistry, College of Natural Science, Sookmyung Women's University, Seoul, 04310, South Korea. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 63.24 kDa 
• Atom Count: 4,416 
• Modeled Residue Count: 554 
• Deposited Residue Count: 570 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5-oxopent-3-ene-1,2,5-tricarboxylate decarboxylase	A, B	285	Exiguobacterium antarcticum B7	Mutation(s): 0  Gene Names: Eab7_1027

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	C [auth A], D [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.269 (Depositor), 0.272 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.205 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.437	α = 90
b = 72.656	β = 101.68
c = 63.374	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-04-03 
Deposition Author(s): Lee, J.H., Lee, C.W.

Revision History  

• Version 1.0: 2019-04-03
  Type: Initial release
  
• Version 1.1: 2024-03-27
  Changes: Data collection, Database references