1EVQ | pdb_00001evq

THE CRYSTAL STRUCTURE OF THE THERMOPHILIC CARBOXYLESTERASE EST2 FROM ALICYCLOBACILLUS ACIDOCALDARIUS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.265 (Depositor), 0.270 (DCC) 
  • R-Value Work: 
    0.216 (Depositor), 0.217 (DCC) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1EVQ

This is version 1.4 of the entry. See complete history

Literature

A snapshot of a transition state analogue of a novel thermophilic esterase belonging to the subfamily of mammalian hormone-sensitive lipase.

De Simone, G.Galdiero, S.Manco, G.Lang, D.Rossi, M.Pedone, C.

(2000) J Mol Biology 303: 761-771

  • DOI: https://doi.org/10.1006/jmbi.2000.4195
  • Primary Citation Related Structures: 
    1EVQ

  • PubMed Abstract: 

    EST2 is a novel thermophilic carboxylesterase, isolated and cloned from Alicyclobacillus (formerly Bacillus) acidocaldarius, which optimally hydrolyses esters with acyl chain lengths of six to eight carbon atoms at 70 degrees C. On the basis of the amino acid sequence homology, it has been classified as a member of the mammalian hormone-sensitive lipase (HSL) subfamily. The crystal structure of EST2, complexed with a sulphonyl derivative, has been determined at 2.6 A resolution by a multiple wavelength anomalous diffraction experiment on a seleno-methionine derivative. EST2 presents a canonical alpha/beta hydrolase core, shielded at the C-terminal side by a cap region built up of five helices. It contains the lipase-like catalytic triad, Ser155, His282 and Asp252, whereby the nucleophile is covalently modified. This allows an unambiguous view of the putative active site of EST2, detecting the oxyanion hole, in whose formation the amino acid sequence motif His81-Gly82-Gly83-Gly84 is involved, and the hydrophobic binding pocket for the acyl chain. The structural model here reported provides the first example of a transition state analogue of an esterase/lipase belonging to the HSL group, thus affording useful information for the design of medical inhibitors. Moreover, as the first X-ray structure of a thermophilic carboxylesterase, the comparison with its mesophilic homologue, the Brefeldin A esterase (BFAE) from Bacillus subtilis, allows the identification of putative determinants of thermal stability.


  • Organizational Affiliation
    • Dipartimento di Chimica and Centro di Studio di Biocristallografia- CNR, University of Naples "Federico II", via Mezzocannone 8, Naples, 80134, Italy.

Macromolecule Content 

  • Total Structure Weight: 34.89 kDa 
  • Atom Count: 2,523 
  • Modeled Residue Count: 308 
  • Deposited Residue Count: 310 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
SERINE HYDROLASE310Alicyclobacillus acidocaldariusMutation(s): 0 
EC: 3.1.1.1
UniProt
Find proteins for Q7SIG1 (Alicyclobacillus acidocaldarius subsp. acidocaldarius)
Explore Q7SIG1 
Go to UniProtKB:  Q7SIG1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7SIG1
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EPE

Query on EPE



Download:Ideal Coordinates CCD File
B [auth A]4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
TRS

Query on TRS



Download:Ideal Coordinates CCD File
C [auth A]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.265 (Depositor), 0.270 (DCC) 
  • R-Value Work:  0.216 (Depositor), 0.217 (DCC) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.105α = 90
b = 79.105β = 90
c = 107.29γ = 90
Software Package:
Software NamePurpose
SOLVEphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-11-22
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-01-31
    Changes: Advisory, Experimental preparation
  • Version 1.4: 2024-12-25
    Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary