+Open data
-Basic information
Entry | Database: PDB / ID: 4xb6 | ||||||
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Title | Structure of the E. coli C-P lyase core complex | ||||||
Components |
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Keywords | TRANSFERASE / protein complex | ||||||
Function / homology | Function and homology information alpha-D-ribose 1-methylphosphonate 5-phosphate C-P-lyase / alpha-D-ribose 1-methylphosphonate 5-phosphate C-P-lyase activity / alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase / alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase activity / alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase complex / carbon phosphorus lyase complex / organic phosphonate metabolic process / organic phosphonate transport / organic phosphonate catabolic process / 4 iron, 4 sulfur cluster binding ...alpha-D-ribose 1-methylphosphonate 5-phosphate C-P-lyase / alpha-D-ribose 1-methylphosphonate 5-phosphate C-P-lyase activity / alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase / alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase activity / alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase complex / carbon phosphorus lyase complex / organic phosphonate metabolic process / organic phosphonate transport / organic phosphonate catabolic process / 4 iron, 4 sulfur cluster binding / lyase activity / protein homodimerization activity / identical protein binding / metal ion binding Similarity search - Function | ||||||
Biological species | Escherichia coli str. K-12 substr. MG1655 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å | ||||||
Authors | Brodersen, D.E. | ||||||
Funding support | Denmark, 1items
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Citation | Journal: Nature / Year: 2015 Title: Structural insights into the bacterial carbon-phosphorus lyase machinery. Authors: Paulina Seweryn / Lan Bich Van / Morten Kjeldgaard / Christopher J Russo / Lori A Passmore / Bjarne Hove-Jensen / Bjarne Jochimsen / Ditlev E Brodersen / Abstract: Phosphorus is required for all life and microorganisms can extract it from their environment through several metabolic pathways. When phosphate is in limited supply, some bacteria are able to use ...Phosphorus is required for all life and microorganisms can extract it from their environment through several metabolic pathways. When phosphate is in limited supply, some bacteria are able to use phosphonate compounds, which require specialized enzymatic machinery to break the stable carbon-phosphorus (C-P) bond. Despite its importance, the details of how this machinery catabolizes phosphonates remain unknown. Here we determine the crystal structure of the 240-kilodalton Escherichia coli C-P lyase core complex (PhnG-PhnH-PhnI-PhnJ; PhnGHIJ), and show that it is a two-fold symmetric hetero-octamer comprising an intertwined network of subunits with unexpected self-homologies. It contains two potential active sites that probably couple phosphonate compounds to ATP and subsequently hydrolyse the C-P bond. We map the binding site of PhnK on the complex using electron microscopy, and show that it binds to a conserved insertion domain of PhnJ. Our results provide a structural basis for understanding microbial phosphonate breakdown. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4xb6.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4xb6.ent.gz | 936.1 KB | Display | PDB format |
PDBx/mmJSON format | 4xb6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xb/4xb6 ftp://data.pdbj.org/pub/pdb/validation_reports/xb/4xb6 | HTTPS FTP |
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-Related structure data
Related structure data | 3033C 2fsuS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit ... , 3 types, 6 molecules AEBFCG
#1: Protein | Mass: 16560.637 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli str. K-12 substr. MG1655 (bacteria) Gene: phnG, b4101, JW4062 / Production host: Escherichia coli (E. coli) / Strain (production host): HO2735 References: UniProt: P16685, alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase #2: Protein | Mass: 21226.506 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Cloning introduced mutation Q152R Source: (gene. exp.) Escherichia coli str. K-12 substr. MG1655 (bacteria) Gene: phnH, b4100, JW4061 / Production host: Escherichia coli (E. coli) / Strain (production host): HO2735 References: UniProt: P16686, alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase #3: Protein | Mass: 38922.707 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Cloning introduced mutation A322V Source: (gene. exp.) Escherichia coli str. K-12 substr. MG1655 (bacteria) Gene: phnI, b4099, JW4060 / Production host: Escherichia coli (E. coli) / Strain (production host): HO2735 References: UniProt: P16687, alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase |
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-Protein , 1 types, 2 molecules DH
#4: Protein | Mass: 31879.088 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli str. K-12 substr. MG1655 (bacteria) Gene: phnJ, b4098, JW4059 / Production host: Escherichia coli (E. coli) / Strain (production host): HO2735 References: UniProt: P16688, alpha-D-ribose 1-methylphosphonate 5-phosphate C-P-lyase |
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-Non-polymers , 3 types, 1800 molecules
#5: Chemical | ChemComp-SO4 / #6: Chemical | ChemComp-ZN / #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.66 % |
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Crystal grow | Temperature: 277 K / Method: batch mode / pH: 7.5 Details: 20% (w/v) PEG 10000, 0.1 M Hepes, pH 7.5, 1 mM trisodium citrate dihydrate, 3% (w/v) 1,8-diaminooctane, and 5 mM 2-mercaptoethanol. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00004 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 6, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00004 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→58.91 Å / Num. obs: 247086 / % possible obs: 99.7 % / Redundancy: 5.6 % / Rsym value: 0.064 / Net I/σ(I): 17.3 |
Reflection shell | Resolution: 1.7→1.74 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 1.7 / Rsym value: 1.038 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: 2FSU Resolution: 1.7→58.36 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.82 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→58.36 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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