[English] 日本語
Yorodumi- PDB-4erp: Crystal structure of a gemcitabine-diphosphate inhibited E. coli ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4erp | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of a gemcitabine-diphosphate inhibited E. coli class Ia ribonucleotide reductase complex | ||||||
Components |
| ||||||
Keywords | OXIDOREDUCTASE / Protein-protein complex / alpha/beta barrel / atp cone / diiron center / RNR alpha / RNR beta / thioredoxin / Ribonucleotide reduction / Cytosol | ||||||
Function / homology | Function and homology information ribonucleoside diphosphate metabolic process / 2'-deoxyribonucleotide biosynthetic process / ribonucleoside-diphosphate reductase complex / nucleobase-containing small molecule interconversion / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / protein folding chaperone / DNA replication / iron ion binding ...ribonucleoside diphosphate metabolic process / 2'-deoxyribonucleotide biosynthetic process / ribonucleoside-diphosphate reductase complex / nucleobase-containing small molecule interconversion / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / protein folding chaperone / DNA replication / iron ion binding / ATP binding / identical protein binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli K-12 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.45 Å | ||||||
Authors | Zimanyi, C.M. / Drennan, C.L. | ||||||
Citation | Journal: Structure / Year: 2012 Title: Tangled up in knots: structures of inactivated forms of E. coli class Ia ribonucleotide reductase. Authors: Christina M Zimanyi / Nozomi Ando / Edward J Brignole / Francisco J Asturias / Joanne Stubbe / Catherine L Drennan / Abstract: Ribonucleotide reductases (RNRs) provide the precursors for DNA biosynthesis and repair and are successful targets for anticancer drugs such as clofarabine and gemcitabine. Recently, we reported that ...Ribonucleotide reductases (RNRs) provide the precursors for DNA biosynthesis and repair and are successful targets for anticancer drugs such as clofarabine and gemcitabine. Recently, we reported that dATP inhibits E. coli class Ia RNR by driving formation of RNR subunits into α4β4 rings. Here, we present the first X-ray structure of a gemcitabine-inhibited E. coli RNR and show that the previously described α4β4 rings can interlock to form an unprecedented (α4β4)2 megacomplex. This complex is also seen in a higher-resolution dATP-inhibited RNR structure presented here, which employs a distinct crystal lattice from that observed in the gemcitabine-inhibited case. With few reported examples of protein catenanes, we use data from small-angle X-ray scattering and electron microscopy to both understand the solution conditions that contribute to concatenation in RNRs as well as present a mechanism for the formation of these unusual structures. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4erp.cif.gz | 775.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4erp.ent.gz | 654.6 KB | Display | PDB format |
PDBx/mmJSON format | 4erp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4erp_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4erp_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 4erp_validation.xml.gz | 189.5 KB | Display | |
Data in CIF | 4erp_validation.cif.gz | 245.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/er/4erp ftp://data.pdbj.org/pub/pdb/validation_reports/er/4erp | HTTPS FTP |
-Related structure data
Related structure data | 5430C 5431C 5432C 5433C 5434C 5435C 5436C 5437C 4ermC 1pfrS 1rlrS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 85877.086 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: b2234, dnaF, JW2228, nrdA / Production host: Escherichia coli (E. coli) References: UniProt: P00452, ribonucleoside-diphosphate reductase #2: Protein | Mass: 43426.863 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: b2235, ftsB, JW2229, nrdB / Production host: Escherichia coli (E. coli) References: UniProt: P69924, ribonucleoside-diphosphate reductase #3: Chemical | ChemComp-ATP / #4: Chemical | ChemComp-FEO / #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.96 Å3/Da / Density % sol: 68.96 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Precipitant solution: 25% PEG 3350, 0.1 M HEPES pH 7.5, 0.2 M ammonium acetate, 5% glycerol mixed 2:1 with protein and streak seeded from crystals grown under similar conditions. , VAPOR ...Details: Precipitant solution: 25% PEG 3350, 0.1 M HEPES pH 7.5, 0.2 M ammonium acetate, 5% glycerol mixed 2:1 with protein and streak seeded from crystals grown under similar conditions. , VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9769 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 11, 2010 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9769 Å / Relative weight: 1 |
Reflection | Resolution: 4.45→50 Å / Num. all: 50820 / Num. obs: 46069 / % possible obs: 90.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 4.45→4.61 Å / Redundancy: 2 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 3528 / Rsym value: 0.357 / % possible all: 70.6 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1RLR and 1PFR Resolution: 4.45→50 Å / Cross valid method: R-free / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 4.45→50 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 4.45→4.61 Å
|