Download MendeleyAutoregulation of the yeast Sir2 deacetylase by reaction and trapping of a pseudosubstrate motif in the active site
Hall, B.E., Buchberger, J.R., Gerber, S.A., Ambrosio, A.L.B., Gygi, S.P., Filman, D., Moazed, D., Ellenberger, T.To be published.
2HJH
Crystal Structure of the Sir2 deacetylase
- PDB DOI: https://doi.org/10.2210/pdb2HJH/pdb
- Classification: HYDROLASE
- Organism(s): Saccharomyces cerevisiae
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2006-06-30 Released: 2008-04-08
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.85 Å
- R-Value Free: 0.215
- R-Value Work: 0.171
This is version 1.3 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| NAD-dependent histone deacetylase SIR2 | 354 | Saccharomyces cerevisiae | Mutation(s): 0 Gene Names: SIR2, MAR1 EC: 3.5.1 (PDB Primary Data), 2.3.1.286 (UniProt) |  | |
UniProt | |||||
Find proteins for P06700 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P06700 Go to UniProtKB: P06700 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P06700 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| XYQ Query on XYQ | D [auth A], G [auth B] | (2R,3R,4S,5R)-5-({[(R)-{[(R)-{[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]OXY}METHYL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL ACETATE C17 H25 N5 O15 P2 IJOUKWCBVUMMCR-DLFWLGJNSA-N |  | ||
| NCA Query on NCA | E [auth A], H [auth B] | NICOTINAMIDE C6 H6 N2 O DFPAKSUCGFBDDF-UHFFFAOYSA-N |  | ||
| ZN Query on ZN | C [auth A], F [auth B] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| MSE Query on MSE | A, B | L-PEPTIDE LINKING | C5 H11 N O2 Se |  | MET |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.85 Å
- R-Value Free: 0.215
- R-Value Work: 0.171
- Space Group: P 1 21 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 52.353 | α = 90 |
| b = 89.566 | β = 104.95 |
| c = 94.51 | γ = 90 |
| Software Name | Purpose |
|---|---|
| DENZO | data reduction |
| SCALEPACK | data scaling |
| SOLVE | phasing |
| RESOLVE | phasing |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| HKL-2000 | data reduction |
Entry History
Deposition Data
- Released Date: 2008-04-08 Deposition Author(s): Hall, B.E., Ellenberger, T.E.
Revision History (Full details and data files)
- Version 1.0: 2008-04-08
Type: Initial release - Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance - Version 1.2: 2017-10-18
Changes: Refinement description - Version 1.3: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Structure summary
