Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 96521.45 
• Atom Count: 6579 
• Residue Count: 878 
• Unique protein chains: 1

2AKZ

Fluoride Inhibition of Enolase: Crystal Structure of the Inhibitory Complex

• DOI: 10.2210/pdb2AKZ/pdb

• Classification: LYASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli


• Deposited: 2005-08-04 Released: 2006-03-21 
• Deposition Author(s): Qin, J., Chai, G., Brewer, J.M., Lovelace, L.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.36 Å
• R-Value Free: 0.144 
• R-Value Work: 0.110 

Literature

Fluoride inhibition of enolase: crystal structure and thermodynamics

Qin, J., Chai, G., Brewer, J.M., Lovelace, L.L., Lebioda, L.

(2006) Biochemistry 45: 793-800

• PubMed: 16411755 
• DOI: 10.1021/bi051558s
• Primary Citation of Related Structures:  
  2AKM


• PubMed Abstract: 
  

Enolase is a dimeric metal-activated metalloenzyme which uses two magnesium ions per subunit: the strongly bound conformational ion and the catalytic ion that binds to the enzyme-substrate complex inducing catalysis. The crystal structure of the human neuronal enolase-Mg2F2P(i) complex (enolase fluoride/phosphate inhibitory complex, EFPIC) determined at 1.36 A resolution shows that the combination of anions effectively mimics an intermediate state in catalysis. The phosphate ion binds in the same site as the phosphate group of the substrate/product, 2-phospho-D-glycerate/phosphoenolpyruvate, and induces binding of the catalytic Mg2+ ion. One fluoride ion bridges the structural and catalytic magnesium ions while the other interacts with the structural magnesium ion and the ammonio groups of Lys 342 and Lys 393. These fluoride ion positions correspond closely to the positions of the oxygen atoms of the substrate's carboxylate moiety. To relate structural changes resulting from fluoride, phosphate, and magnesium ions binding to those that are induced by phosphate and magnesium ions alone, we also determined the structure of the human neuronal enolase-Mg2P(i) complex (enolase phosphate inhibitory complex, EPIC) at 1.92 A resolution. It shows the closed conformation in one subunit and a mixture of open and semiclosed conformations in the other. The EPFIC dimer is essentially symmetric while the EPIC dimer is asymmetric. Isothermal titration calorimetry data confirmed binding of four fluoride ions per dimer and yielded Kb values of 7.5 x 10(5) +/- 1.3 x 10(5), 1.2 x 10(5) +/- 0.2 x 10(5), 8.6 x 10(4) +/- 1.6 x 10(4), and 1.6 x 10(4) +/- 0.7 x 10(4) M(-1). The different binding constants indicate negative cooperativity between the subunits; the asymmetry of EPIC supports such an interpretation.

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Organizational Affiliation: 

Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Gamma enolase	A, B	439	Homo sapiens	Mutation(s): 0  Gene Names: ENO2 EC: 4.2.1.11
Find proteins for P09104 (Homo sapiens) Go to Gene View: ENO2 Go to UniProtKB:  P09104

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
PO4	A, B	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
F	A, B	FLUORIDE ION F KRHYYFGTRYWZRS-UHFFFAOYSA-M
MG	A, B	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
TRS	A	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL TRIS BUFFER C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.36 Å
• R-Value Free: 0.144 
• R-Value Work: 0.110 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length (Å)	Angle (°)
a = 109.007	α = 90.00
b = 118.515	β = 90.00
c = 67.189	γ = 90.00

Software Package:

Software Name	Purpose
HKL-2000	data reduction
HKL-2000	data scaling
SHELX	model building
SHELXL-97	refinement
SHELXS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-08-04 
• Released Date: 2006-03-21 
• Deposition Author(s): Qin, J., Chai, G., Brewer, J.M., Lovelace, L.L.

Revision History 

• Version 1.0: 2006-03-21
  Type: Initial release
• Version 1.1: 2008-04-30
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance