4XXF | pdb_00004xxf

L-fuculose 1-phosphate aldolase from Glaciozyma antarctica PI12

• PDB DOI: https://doi.org/10.2210/pdb4XXF/pdb

• Classification: LYASE
• Organism(s): Glaciozyma antarctica
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-01-30 Released: 2015-02-25 
• Deposition Author(s): Jaafar, N.R., Abu Bakar, F.D., Abdul Murad, A.M., Illias, R., Littler, D., Beddoe, T., Rossjohn, J., Mahadi, M.N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.34 Å
• R-Value Free: 
  0.187 (Depositor), 0.189 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.174 (DCC) 
• R-Value Observed: 
  0.172 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of fuculose aldolase from the Antarctic psychrophilic yeast Glaciozyma antarctica PI12.

Jaafar, N.R., Littler, D., Beddoe, T., Rossjohn, J., Illias, R.M., Mahadi, N.M., Mackeen, M.M., Murad, A.M., Abu Bakar, F.D.

(2016) Acta Crystallogr F Struct Biol Commun 72: 831-839

• PubMed: 27827354 
• DOI: https://doi.org/10.1107/S2053230X16015612
• Primary Citation Related Structures: 
  4XXF


• PubMed Abstract: 
  

  Fuculose-1-phosphate aldolase (FucA) catalyses the reversible cleavage of L-fuculose 1-phosphate to dihydroxyacetone phosphate (DHAP) and L-lactaldehyde. This enzyme from mesophiles and thermophiles has been extensively studied; however, there is no report on this enzyme from a psychrophile. In this study, the gene encoding FucA from Glaciozyma antarctica PI12 (GaFucA) was cloned and the enzyme was overexpressed in Escherichia coli, purified and crystallized. The tetrameric structure of GaFucA was determined to 1.34 Å resolution. The overall architecture of GaFucA and its catalytically essential histidine triad are highly conserved among other fuculose aldolases. Comparisons of structural features between GaFucA and its mesophilic and thermophilic homologues revealed that the enzyme has typical psychrophilic attributes, indicated by the presence of a high number of nonpolar residues at the surface and a lower number of arginine residues.

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Organizational Affiliation: 
• School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor Darul Ehsan 43600, Malaysia.
Infection and Immunity Program and the Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Victoria 3800, Australia.
Department of Bioprocess Engineering, Faculty of Chemical Engineering, Universiti Teknologi Malaysia, 81310 Skudai, Johor Darul Takzim, Malaysia.
Malaysia Genome Institute, Jalan Bangi Lama, 43000 Kajang, Selangor Darul Ehsan, Malaysia.
Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor Darul Ehsan, Malaysia.

Biological Assembly 1  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 28.24 kDa 
• Atom Count: 2,218 
• Modeled Residue Count: 249 
• Deposited Residue Count: 258 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fuculose-1-phosphate aldolase	A	258	Glaciozyma antarctica	Mutation(s): 0  EC: 4.1.2.17
UniProt
Find proteins for A0A0J9X279 (Glaciozyma antarctica) Explore A0A0J9X279  Go to UniProtKB:  A0A0J9X279

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.34 Å
• R-Value Free:  0.187 (Depositor), 0.189 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.174 (DCC) 
• R-Value Observed: 0.172 (Depositor) 

Space Group: P 4 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.33	α = 90
b = 84.33	β = 90
c = 78.5	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Coot	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2015-02-25 
Deposition Author(s): Jaafar, N.R., Abu Bakar, F.D., Abdul Murad, A.M., Illias, R., Littler, D., Beddoe, T., Rossjohn, J., Mahadi, M.N.

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Funding Organization	Location	Grant Number
	Malaysia	--

Revision History  

• Version 1.0: 2015-02-25
  Type: Initial release
  
• Version 1.1: 2015-09-02
  Changes: Data collection
• Version 1.2: 2016-11-16
  Changes: Database references
• Version 1.3: 2019-12-25
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description