7ATD

Structure of inactive EstD11 S144A in complex with methyl-naproxen


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.168 

Starting Model: experimental
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This is version 2.2 of the entry. See complete history


Literature

Biochemical and Structural Characterization of a novel thermophilic esterase EstD11 provide catalytic insights for the HSL family.

Miguel-Ruano, V.Rivera, I.Rajkovic, J.Knapik, K.Torrado, A.Otero, J.M.Beneventi, E.Becerra, M.Sanchez-Costa, M.Hidalgo, A.Berenguer, J.Gonzalez-Siso, M.I.Cruces, J.Rua, M.L.Hermoso, J.A.

(2021) Comput Struct Biotechnol J 19: 1214-1232

  • DOI: https://doi.org/10.1016/j.csbj.2021.01.047
  • Primary Citation of Related Structures:  
    7AT0, 7AT2, 7AT3, 7AT4, 7ATD, 7ATF, 7ATQ, 7AUY, 7AV5, 7NB5

  • PubMed Abstract: 

    A novel esterase, EstD11, has been discovered in a hot spring metagenomic library. It is a thermophilic and thermostable esterase with an optimum temperature of 60°C. A detailed substrate preference analysis of EstD11 was done using a library of chromogenic ester substrate that revealed the broad substrate specificity of EstD11 with significant measurable activity against 16 substrates with varied chain length, steric hindrance, aromaticity and flexibility of the linker between the carboxyl and the alcohol moiety of the ester. The tridimensional structures of EstD11 and the inactive mutant have been determined at atomic resolutions. Structural and bioinformatic analysis, confirm that EstD11 belongs to the family IV, the hormone-sensitive lipase (HSL) family, from the α/β-hydrolase superfamily. The canonical α/β-hydrolase domain is completed by a cap domain, composed by two subdomains that can unmask of the active site to allow the substrate to enter. Eight crystallographic complexes were solved with different substrates and reaction products that allowed identification of the hot-spots in the active site underlying the specificity of the protein. Crystallization and/or incubation of EstD11 at high temperature provided unique information on cap dynamics and a first glimpse of enzymatic activity in vivo . Very interestingly, we have discovered a unique Met zipper lining the active site and the cap domains that could be essential in pivotal aspects as thermo-stability and substrate promiscuity in EstD11.


  • Organizational Affiliation

    Department of Crystallography and Structural Biology, Institute of Physical-Chemistry "Rocasolano", Spanish National Research Council (CSIC), Madrid, Spain.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
EstD11 S144A
A, B
296uncultured bacteriumMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
RXH (Subject of Investigation/LOI)
Query on RXH

Download Ideal Coordinates CCD File 
Q [auth B]Naproxen Methyl Ester
C15 H16 O3
ZFYFBPCRUQZGJE-JTQLQIEISA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
I [auth A],
S [auth B]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
FMT
Query on FMT

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
R [auth B]
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.168 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.846α = 90
b = 80.243β = 90
c = 145.146γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Spanish Ministry of Economy and CompetitivenessSpainBFU2017-90030-P

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-03
    Type: Initial release
  • Version 2.0: 2021-03-17
    Changes: Database references, Non-polymer description
  • Version 2.1: 2022-02-02
    Changes: Data collection, Database references
  • Version 2.2: 2024-01-31
    Changes: Data collection, Derived calculations, Refinement description