6BFY

Crystal structure of enolase from Escherichia coli with bound 2-phosphoglycerate substrate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.169 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structural and Functional Studies of Bacterial Enolase, a Potential Target against Gram-Negative Pathogens.

Krucinska, J.Falcone, E.Erlandsen, H.Hazeen, A.Lombardo, M.N.Estrada, A.Robinson, V.L.Anderson, A.C.Wright, D.L.

(2019) Biochemistry 58: 1188-1197

  • DOI: https://doi.org/10.1021/acs.biochem.8b01298
  • Primary Citation of Related Structures:  
    6BFY, 6BFZ

  • PubMed Abstract: 

    Enolase is a glycolytic metalloenzyme involved in carbon metabolism. The advantage of targeting enolase lies in its essentiality in many biological processes such as cell wall formation and RNA turnover and as a plasminogen receptor. We initially used a DARTS assay to identify enolase as a target in Escherichia coli. The antibacterial activities of α-, β-, and γ-substituted seven-member ring tropolones were first evaluated against four strains representing a range of Gram-negative bacteria. We observed that the chemical properties and position of the substituents on the tropolone ring play an important role in the biological activity of the investigated compounds. Both α- and β-substituted phenyl derivatives of tropolone were the most active with minimum inhibitory concentrations in the range of 11-14 μg/mL. The potential inhibitory activity of the synthetic tropolones was further evaluated using an enolase inhibition assay, X-ray crystallography, and molecular docking simulations. The catalytic activity of enolase was effectively inhibited by both the naturally occurring β-thujaplicin and the α- and β-substituted phenyl derivatives of tropolones with IC 50 values in range of 8-11 μM. Ligand binding parameters were assessed by isothermal titration calorimetry and differential scanning calorimetry techniques and agreed with the in vitro data. Our studies validate the antibacterial potential of tropolones with careful consideration of the position and character of chelating moieties for stronger interaction with metal ions and residues in the enolase active site.


  • Organizational Affiliation

    Department of Pharmaceutical Sciences , University of Connecticut , 69 North Eagleville Road , Storrs , Connecticut 06269 , United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Enolase449Escherichia coliMutation(s): 0 
Gene Names: enoECS88_3047
EC: 4.2.1.11
UniProt
Find proteins for P0A6P9 (Escherichia coli (strain K12))
Explore P0A6P9 
Go to UniProtKB:  P0A6P9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A6P9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
2PG
Query on 2PG

Download Ideal Coordinates CCD File 
EA [auth F]
G [auth A]
KA [auth D]
O [auth B]
QA [auth E]
EA [auth F],
G [auth A],
KA [auth D],
O [auth B],
QA [auth E],
W [auth C]
2-PHOSPHOGLYCERIC ACID
C3 H7 O7 P
GXIURPTVHJPJLF-UWTATZPHSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth C]
BA [auth C]
CA [auth C]
DA [auth C]
HA [auth F]
AA [auth C],
BA [auth C],
CA [auth C],
DA [auth C],
HA [auth F],
J [auth A],
JA [auth D],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
NA [auth D],
PA [auth E],
R [auth B],
S [auth B],
T [auth B],
TA [auth E],
U [auth B],
UA [auth E],
V [auth B],
VA [auth E],
Z [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
IA [auth F],
OA [auth D],
WA [auth E]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
FA [auth F]
GA [auth F]
H [auth A]
I [auth A]
LA [auth D]
FA [auth F],
GA [auth F],
H [auth A],
I [auth A],
LA [auth D],
MA [auth D],
P [auth B],
Q [auth B],
RA [auth E],
SA [auth E],
X [auth C],
Y [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.169 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.94α = 90
b = 142.4β = 90
c = 206.64γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-31
    Type: Initial release
  • Version 1.1: 2019-03-13
    Changes: Data collection, Database references
  • Version 1.2: 2019-03-20
    Changes: Data collection, Database references
  • Version 1.3: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description