[English] 日本語
Yorodumi- PDB-6mv9: X-ray crystal structure of Bacillus subtilis ribonucleotide reduc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6mv9 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | X-ray crystal structure of Bacillus subtilis ribonucleotide reductase NrdE alpha subunit with TTP and ADP | |||||||||
Components | Ribonucleoside-diphosphate reductaseRibonucleotide reductase | |||||||||
Keywords | OXIDOREDUCTASE / ribonucleotide reductase / allostery / nucleotide metabolism / dATP / ATP | |||||||||
Function / homology | Function and homology information ribonucleoside-diphosphate reductase complex / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / DNA replication / ATP binding Similarity search - Function | |||||||||
Biological species | Bacillus subtilis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å | |||||||||
Authors | Thomas, W.C. / Brooks, F.P. / Bacik, J.P. / Ando, N. | |||||||||
Funding support | United States, 2items
| |||||||||
Citation | Journal: Nat Commun / Year: 2019 Title: Convergent allostery in ribonucleotide reductase. Authors: William C Thomas / F Phil Brooks / Audrey A Burnim / John-Paul Bacik / JoAnne Stubbe / Jason T Kaelber / James Z Chen / Nozomi Ando / Abstract: Ribonucleotide reductases (RNRs) use a conserved radical-based mechanism to catalyze the conversion of ribonucleotides to deoxyribonucleotides. Within the RNR family, class Ib RNRs are notable for ...Ribonucleotide reductases (RNRs) use a conserved radical-based mechanism to catalyze the conversion of ribonucleotides to deoxyribonucleotides. Within the RNR family, class Ib RNRs are notable for being largely restricted to bacteria, including many pathogens, and for lacking an evolutionarily mobile ATP-cone domain that allosterically controls overall activity. In this study, we report the emergence of a distinct and unexpected mechanism of activity regulation in the sole RNR of the model organism Bacillus subtilis. Using a hypothesis-driven structural approach that combines the strengths of small-angle X-ray scattering (SAXS), crystallography, and cryo-electron microscopy (cryo-EM), we describe the reversible interconversion of six unique structures, including a flexible active tetramer and two inhibited helical filaments. These structures reveal the conformational gymnastics necessary for RNR activity and the molecular basis for its control via an evolutionarily convergent form of allostery. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6mv9.cif.gz | 278.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6mv9.ent.gz | 222.1 KB | Display | PDB format |
PDBx/mmJSON format | 6mv9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mv/6mv9 ftp://data.pdbj.org/pub/pdb/validation_reports/mv/6mv9 | HTTPS FTP |
---|
-Related structure data
Related structure data | 9272C 9293C 6mt9C 6mveC 6mw3C 6myxC 6cgmS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 80791.469 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: nrdE_1, B4417_3413, NCTC3610_03984 / Plasmid: pE-SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: A0A162Q3J9, UniProt: P50620*PLUS, ribonucleoside-diphosphate reductase #2: Chemical | #3: Chemical | #4: Chemical | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.02 Å3/Da / Density % sol: 59.24 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.6 Details: The crystal was grown by vapor diffusion from 4.5 mg/ml holo-NrdE in 50 mM HEPES (pH 7.6), 50 mM NaCl, 5 mM MgCl2, 2 mM TCEP, and 1% glycerol, supplemented with 5 mM ATP, 0.5 mM TTP, and 5 ...Details: The crystal was grown by vapor diffusion from 4.5 mg/ml holo-NrdE in 50 mM HEPES (pH 7.6), 50 mM NaCl, 5 mM MgCl2, 2 mM TCEP, and 1% glycerol, supplemented with 5 mM ATP, 0.5 mM TTP, and 5 mM CDP. The protein solution was incubated for 10 minutes with freshly added nucleotides prior to being mixed in a 1:1 hanging drop with a precipitating solution of 6% PEG 3350, 1% w/v tryptone, and 50 mM HEPES at pH 6.9. Crystals were cryoprotected by soaking for 5-10 seconds in well solution mixed with 8% w/v sucrose, 2% w/v glucose, 8% v/v glycerol, 8% v/v ethylene glycol and supplemented with nucleotides, TCEP, and MgCl2 adjusted to the same concentrations used in the original protein solutions. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9775 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 6, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9775 Å / Relative weight: 1 |
Reflection | Resolution: 2.95→19.98 Å / Num. obs: 41464 / % possible obs: 99.2 % / Redundancy: 3.6 % / CC1/2: 0.978 / Rmerge(I) obs: 0.18 / Rpim(I) all: 0.108 / Net I/σ(I): 5.4 |
Reflection shell | Resolution: 2.95→3.07 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.763 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4649 / CC1/2: 0.441 / Rpim(I) all: 0.452 / % possible all: 99.8 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6CGM Resolution: 2.95→19.975 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.37
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.95→19.975 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|