2DQY | pdb_00002dqy

Crystal structure of human carboxylesterase in complex with cholate and palmitate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 
    0.271 (Depositor) 
  • R-Value Work: 
    0.226 (Depositor) 
  • R-Value Observed: 
    0.226 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 2DQY

This is version 1.5 of the entry. See complete history

Literature

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 Biology 363: 201-214

  • DOI: https://doi.org/10.1016/j.jmb.2006.08.025
  • Primary Citation 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.

Macromolecule Content 

  • Total Structure Weight: 183.53 kDa 
  • Atom Count: 12,967 
  • Modeled Residue Count: 1,596 
  • Deposited Residue Count: 1,626 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Liver carboxylesterase 1
A, B, C
542Homo sapiensMutation(s): 0 
EC: 3.1.1.1 (PDB Primary Data), 3.1.1.56 (UniProt), 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
GTEx:  ENSG00000198848 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23141
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P23141-1
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CHD

Query on CHD



Download:Ideal Coordinates CCD File
I [auth A],
N [auth B],
T [auth C]
CHOLIC ACID
C24 H40 O5
BHQCQFFYRZLCQQ-OELDTZBJSA-N
SIA

Query on SIA



Download:Ideal Coordinates CCD File
E [auth A],
L [auth B],
Q [auth C]
N-acetyl-alpha-neuraminic acid
C11 H19 N O9
SQVRNKJHWKZAKO-YRMXFSIDSA-N
PLM

Query on PLM



Download:Ideal Coordinates CCD File
J [auth A],
O [auth B],
U [auth C]
PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
NAG

Query on NAG



Download:Ideal Coordinates CCD File
D [auth A],
K [auth B],
P [auth C]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
F [auth A]
G [auth A]
H [auth A]
M [auth B]
R [auth C]
F [auth A],
G [auth A],
H [auth A],
M [auth B],
R [auth C],
S [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free:  0.271 (Depositor) 
  • R-Value Work:  0.226 (Depositor) 
  • R-Value Observed: 0.226 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.292α = 90
b = 179.877β = 90
c = 201.323γ = 90
Software Package:
Software NamePurpose
CNSrefinement
CrystalCleardata reduction
MOSFLMdata reduction
AMoREphasing

Structure Validation

View Full Validation Report



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 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary
  • Version 1.4: 2023-10-25
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 1.5: 2024-11-20
    Changes: Structure summary