5A7F

Comparison of the structure and activity of glycosylated and aglycosylated Human Carboxylesterase 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.160 

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This is version 1.2 of the entry. See complete history


Literature

Comparison of the Structure and Activity of Glycosylated and Aglycosylated Human Carboxylesterase 1.

Arena De Souza, V.Scott, D.J.Nettleship, J.E.Rahman, N.Charlton, M.H.Walsh, M.A.Owens, R.J.

(2015) PLoS One 10: 43919

  • DOI: 10.1371/journal.pone.0143919
  • Primary Citation of Related Structures:  
    5A7F, 5A7G, 5A7H

  • PubMed Abstract: 
  • Human Carboxylesterase 1 (hCES1) is the key liver microsomal enzyme responsible for detoxification and metabolism of a variety of clinical drugs. To analyse the role of the single N-linked glycan on the structure and activity of the enzyme, authentically glycosylated and aglycosylated hCES1, generated by mutating asparagine 79 to glutamine, were produced in human embryonic kidney cells ...

    Human Carboxylesterase 1 (hCES1) is the key liver microsomal enzyme responsible for detoxification and metabolism of a variety of clinical drugs. To analyse the role of the single N-linked glycan on the structure and activity of the enzyme, authentically glycosylated and aglycosylated hCES1, generated by mutating asparagine 79 to glutamine, were produced in human embryonic kidney cells. Purified enzymes were shown to be predominantly trimeric in solution by analytical ultracentrifugation. The purified aglycosylated enzyme was found to be more active than glycosylated hCES1 and analysis of enzyme kinetics revealed that both enzymes exhibit positive cooperativity. Crystal structures of hCES1 a catalytically inactive mutant (S221A) and the aglycosylated enzyme were determined in the absence of any ligand or substrate to high resolutions (1.86 Å, 1.48 Å and 2.01 Å, respectively). Superposition of all three structures showed only minor conformational differences with a root mean square deviations of around 0.5 Å over all Cα positions. Comparison of the active sites of these un-liganded enzymes with the structures of hCES1-ligand complexes showed that side-chains of the catalytic triad were pre-disposed for substrate binding. Overall the results indicate that preventing N-glycosylation of hCES1 does not significantly affect the structure or activity of the enzyme.


    Organizational Affiliation

    Division of Structural Biology, Henry Wellcome Building for Genomic Medicine, University of Oxford, Roosevelt Drive, Oxford, United Kingdom.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
LIVER CARBOXYLESTERASE 1A532Homo sapiensMutation(s): 0 
Gene Names: CES1CES2SES1
EC: 3.1.1.1 (PDB Primary Data), 3.1.1.56 (PDB Primary Data), 3.1.1.13 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P23141 (Homo sapiens)
Explore P23141 
Go to UniProtKB:  P23141
PHAROS:  P23141
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23141
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
B [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
PO4
Query on PO4

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.160 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.715α = 90
b = 114.715β = 90
c = 117.78γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata 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: 2016-01-13
    Type: Initial release
  • Version 1.1: 2019-05-15
    Changes: Data collection, Derived calculations, Experimental preparation, Other
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Other, Structure summary