Crystal structure of human carboxylesterase in complex with Coenzyme A

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.183 

wwPDB Validation   3D Report Full Report

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Multisite promiscuity in the processing of endogenous substrates by human carboxylesterase 1

Bencharit, S.Edwards, C.C.Morton, C.L.Howard-Williams, E.L.Kuhn, P.Potter, P.M.Redinbo, M.R.

(2006) J Mol Biol 363: 201-214

  • DOI: https://doi.org/10.1016/j.jmb.2006.08.025
  • Primary Citation of Related Structures:  
    2DQY, 2DQZ, 2DR0, 2H7C

  • PubMed Abstract: 

    Human carboxylesterase 1 (hCE1) is a drug and endobiotic-processing serine hydrolase that exhibits relatively broad substrate specificity. It has been implicated in a variety of endogenous cholesterol metabolism pathways including the following apparently disparate reactions: cholesterol ester hydrolysis (CEH), fatty acyl Coenzyme A hydrolysis (FACoAH), acyl-Coenzyme A:cholesterol acyltransfer (ACAT), and fatty acyl ethyl ester synthesis (FAEES). The structural basis for the ability of hCE1 to perform these catalytic actions involving large substrates and products has remained unclear. Here we present four crystal structures of the hCE1 glycoprotein in complexes with the following endogenous substrates or substrate analogues: Coenzyme A, the fatty acid palmitate, and the bile acids cholate and taurocholate. While the active site of hCE1 was known to be promiscuous and capable of interacting with a variety of chemically distinct ligands, these structures reveal that the enzyme contains two additional ligand-binding sites and that each site also exhibits relatively non-specific ligand-binding properties. Using this multisite promiscuity, hCE1 appears structurally capable of assembling several catalytic events depending, apparently, on the physiological state of the cellular environment. These results expand our understanding of enzyme promiscuity and indicate that, in the case of hCE1, multiple non-specific sites are employed to perform distinct catalytic actions.

  • Organizational Affiliation

    Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Liver carboxylesterase 1
A, B, C, D, E
A, B, C, D, E, F
542Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P23141 (Homo sapiens)
Explore P23141 
Go to UniProtKB:  P23141
PHAROS:  P23141
GTEx:  ENSG00000198848 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23141
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
G, H
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on COA

Download Ideal Coordinates CCD File 
CA [auth E]
FA [auth F]
K [auth A]
O [auth B]
S [auth C]
CA [auth E],
FA [auth F],
K [auth A],
O [auth B],
S [auth C],
Y [auth D]
C21 H36 N7 O16 P3 S
Query on SIA

Download Ideal Coordinates CCD File 
AA [auth E],
U [auth D]
N-acetyl-alpha-neuraminic acid
C11 H19 N O9
Query on NAG

Download Ideal Coordinates CCD File 
L [auth B],
P [auth C],
T [auth D],
Z [auth E]
C8 H15 N O6
Query on SO4

Download Ideal Coordinates CCD File 
BA [auth E]
DA [auth F]
EA [auth F]
I [auth A]
J [auth A]
BA [auth E],
DA [auth F],
EA [auth F],
I [auth A],
J [auth A],
M [auth B],
N [auth B],
Q [auth C],
R [auth C],
V [auth D],
W [auth D],
X [auth D]
O4 S
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.183 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.99α = 90
b = 115.37β = 90.05
c = 175.53γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
MOSFLMdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-08-29
    Type: Initial release
  • Version 1.1: 2007-10-22
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2023-10-25
    Changes: Data collection, Database references, Refinement description, Structure summary