| Literature DB >> 26657071 |
Victoria Arena de Souza1,2,3, David J Scott4,5, Joanne E Nettleship1,2, Nahid Rahman1,2, Michael H Charlton6, Martin A Walsh4,3, Raymond J Owens1,2.
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. 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.Entities:
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Year: 2015 PMID: 26657071 PMCID: PMC4676782 DOI: 10.1371/journal.pone.0143919
Source DB: PubMed Journal: PLoS One ISSN: 1932-6203 Impact factor: 3.240
Data collection and refinement statistics.
| hCES1 wild type | hCES1 S221A | hCES1 N79Q | |
|---|---|---|---|
| Data Collection | |||
| X-Ray Source | DLS, I04 | DLS, I03 | DLS, I04 |
| Wavelength (Å) | 0.9795 | 0.97625 | 0.9795 |
| Space Group | R3: H | R3: H | R3: H |
| Unit Cell Parameters | |||
| a, b, c [Å] | 114.72, 114.72, 117.78 | 115.39, 115.39, 128.14 | 115.47, 115.47, 127.28 |
| α, β, γ [°] | 90, 90, 120 | 90, 90, 120 | 90, 90, 120 |
| Resolution range [Å] | 50.00–1.86 (1.88–1.86) | 53.94–1.48 (1.52–1.48) | 78.63–2.01 (2.06–2.01) |
| Completeness (%) | 97.0 (71.5) | 98.4 (91.8) | 98.3 (98.0) |
| Rmerge | 6.5 (43.3) | 4.7 (69) | 6.3 (61) |
| CC1/2 | 0.785 | 0.612 | 0.64 |
| <I>/σ(<I>) | 17.4 (1.8) | 11.1 (1.0) | 9.7 (1.3) |
| Multiplicity | 2.8 (2.3) | 2.9 (2.0) | 3.0 (3.0) |
| Data Refinement | |||
| No. of reflections | 132,450 | 303,901 | 125,184 |
| No. of unique reflections | 46, 879 | 104,388 | 41,414 |
| R-factor | 15.83 | 12.96 | 17.9 |
| Rfree | 18.76 | 17.19 | 22.16 |
| R.m.s. deviations | |||
| Bond lengths (Å) | 0.013 | 0.012 | 0.012 |
| Bond angles (°) | 1.63 | 1.51 | 1.4694 |
| Wilson B-factor (Å2) | 21 | 19.4 | 19.2 |
| Mean B-factor (Å2) | 18.7 | 31 | 43.37 |
aValues in parentheses refer to data in the highest resolution shell for each protein.
bRmerge = ∑ ∑|I − 〈I 〉|/∑ ∑ I .
cCC values are the half-set correlation coefficients as described by Karplus & Diederichs [49]
dR-factor = ||F | − |F ||/∑|F |;
eRfree = R-factor for a selected subset (5%) of the reflections that were not included in prior refinement calculation.
Fig 1Purification of human carboxylesterases.
(a) Size exclusion profiles of purified hCES1 (blue trace) hCES1 N79Q (green trace) and hCES1 S221A (red trace) enzymes from media of transfected HEK cells. Samples were run on a HiLoad 16/60Superdex 200 column (GE Healthcare) in 200 mM NaCl, 20 mM Tris-HCl, pH 7.5. The peak corresponds to a molecular weight of approximately 160 kDa as estimated from the elution volumes of globular proteins of known molecular weight: Aprotinin (6.5 kDa) Ribonuclease A (13.7 kDa) Carbonic Anhydrase (29 kDa), Ovalbumin (44 kDa), Conalbumin (75 kDa) Aldolase (158 kDa) Ferritin (440 kDa) and Blue Dextran 2000. (b) SDS-polyacrylamide gel of purified CES1 (lanes 1 and 2) and CES1 N79Q (lanes 3 and 4) untreated (lanes 1 and 3) and treated with PNGaseF (lanes 2 and 4). (c) The sedimentation velocity distribution for hCES1 N79Q. Data for hCES1 and hCES1 S221A gave the same profiles.
Fig 2Enzyme activity of human carboxylesterases.
Plots of initial rates of reaction against enzyme concentration assayed as described in the Methods section at a substrate concentration of 750 μM 4-NPA (a) CES1 (b) CES1 N79Q. Plots of initial reaction rates against substrate concentration for the hydrolysis of 4-NPA by (c) hCES1 and (d) hCES1 N79Q (3.4 nM each enzyme). The molarity of the enzyme was calculated assuming 100% trimer with a molecular weight of 182.7 kDa.
Enzyme kinetic data.
| Parameter | CES1 | CES1 N79Q |
|---|---|---|
| Vmax (μMmin-1) | 9.25 +/- 1.30 | 10.92 +/- 2.01 |
| h | 1.46 +/- 0.26 | 1.57 +/- 0.4 |
| Khalf (μM) | 1123 +/- 280.2 | 1090 +/- 343.3 |
| Goodness of Fit (r2) | 0.9915 | 0.9819 |
Values are given +/- standard errors from the analysis of V0 vs S using the allosteric model in GraphPad Prism version 6
Fig 3Crystal structures of human carboxylesterases.
(a) Overlay of hCES1 (blue) and hCES1 N79Q (gold) (b) Views of the glycosylation site for hCES1, S122A hCES1 and the N79Q mutant. The Fo–Fc omit map electron density is shown carved around the glycosylation site (N79) and contoured at a level of 3 σ (c) Trimer of hCES1 generated by the space group symmetry, N-acetylglucosamine sugars attached to N97 of hCES1 are represented as spheres in red and green (d) Superpostion of the catalytic triad of hCES1 (mauve), hCES1 N79Q (green), hCES1 S221A (yellow) hCES1 tamoxifen complex (PDB id 1ya4, turquoise). Residues are in stick representation. The bound tamoxifen is coloured turquoise. (e) Cartoon representation of the hCES1 trimer generated by the space group symmetry with the K78:E183 and K275:E292 salt bridges shown in spheres (K78 in green, E183 in magenta, K275 in cyan and E292 in orange).
Structure alignment of human hCES1.
| RMSD (Å) | |||
|---|---|---|---|
| hCES1 | Wild type | S221A | N79Q |
|
| - | 0.44 | 0.47 |
|
| - | - | 0.30 |
|
| 0.50 | 0.48 | 0.48 |
|
| 0.52 | 0.57 | 0.56 |
|
| 0.72 | 0.70 | 0.68 |
The structures were aligned using the PDBeFold server and the RMSD calculated between all Ca-atoms at best 3D superposition of the query and target structures (*average from all chains in the asymmetric unit).