Download MendeleyStructural Basis for Base Engagement and Stereochemistry Revealed by Alteration of Catalytic Residue Glu43 in DNA Repair Glycosylase MutY
Russelburg, L.P., Demir, M., Cedeno, K., David, S.S., Horvath, M.P.To be published.
8DWF
Glycosylase MutY variant E43S in complex with DNA containing d(8-oxo-G) paired with substrate adenine
- PDB DOI: https://doi.org/10.2210/pdb8DWF/pdb
- NAKB: 8DWF
- Classification: HYDROLASE/DNA
- Organism(s): Geobacillus stearothermophilus, synthetic construct
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): Yes
- Deposited: 2022-08-01 Released: 2023-08-09
- Funding Organization(s): National Science Foundation (NSF, United States)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.60 Å
- R-Value Free: 0.253
- R-Value Work: 0.207
- R-Value Observed: 0.208
wwPDB Validation 3D Report Full Report
This is version 1.0 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 |
| Adenine DNA glycosylase | 365 | Geobacillus stearothermophilus | Mutation(s): 1 Gene Names: mutY EC: 3.2.2.31 |  | |
UniProt | |||||
Find proteins for P83847 (Geobacillus stearothermophilus) Explore P83847 Go to UniProtKB: P83847 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P83847 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar nucleic acids by: Sequence | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| DNA (5'-D(*AP*AP*GP*AP*CP*(8OG)P*TP*GP*GP*AP*C)-3') | 11 | synthetic construct |  | ||
Sequence AnnotationsExpand | |||||
| |||||
Find similar nucleic acids by: Sequence | 3D Structure
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| DNA (5'-D(*TP*GP*TP*CP*CP*AP*AP*GP*TP*CP*T)-3') | 11 | synthetic construct |  | ||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| SF4 (Subject of Investigation/LOI) Query on SF4 | G [auth A], L [auth D] | IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N |  | ||
| TRS Query on TRS | K [auth B], P [auth E] | 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O |  | ||
| EDO Query on EDO | J [auth A], O [auth D] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |  | ||
| CA Query on CA | H [auth A], I [auth A], M [auth D], N [auth D] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.60 Å
- R-Value Free: 0.253
- R-Value Work: 0.207
- R-Value Observed: 0.208
- Space Group: P 1 21 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 49.08 | α = 90 |
| b = 137.9 | β = 101.44 |
| c = 74.52 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| XDS | data reduction |
| XSCALE | data scaling |
| PHENIX | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2023-08-09 Deposition Author(s): Russelburg, L.P., Demir, M., David, S.S., Horvath, M.P.
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Science Foundation (NSF, United States) | United States | 1905304 |
| National Science Foundation (NSF, United States) | United States | 1905249 |
| National Science Foundation (NSF, United States) | United States | 1610721 |
| National Science Foundation (NSF, United States) | United States | 1608934 |
Revision History (Full details and data files)
- Version 1.0: 2023-08-09
Type: Initial release
