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Open data
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Basic information
Entry | Database: PDB / ID: 6hwj | ||||||
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Title | Glucosamine kinase (crystal form A) | ||||||
![]() | Glucosamine kinase | ||||||
![]() | TRANSFERASE / Glucosamine kinase | ||||||
Function / homology | ![]() glucosamine kinase / glucosamine kinase activity / carbohydrate metabolic process / phosphorylation / magnesium ion binding / ATP binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Manso, J.A. / Pereira, P.J.B. | ||||||
![]() | ![]() Title: Molecular Fingerprints for a Novel Enzyme Family in with Glucosamine Kinase Activity. Authors: José A Manso / Daniela Nunes-Costa / Sandra Macedo-Ribeiro / Nuno Empadinhas / Pedro José Barbosa Pereira / ![]() Abstract: have long been the main source of antibiotics, secondary metabolites with tightly controlled biosynthesis by environmental and physiological factors. Phosphorylation of exogenous glucosamine has ... have long been the main source of antibiotics, secondary metabolites with tightly controlled biosynthesis by environmental and physiological factors. Phosphorylation of exogenous glucosamine has been suggested as a mechanism for incorporation of this extracellular material into secondary metabolite biosynthesis, but experimental evidence of specific glucosamine kinases in is lacking. Here, we present the molecular fingerprints for the identification of a unique family of actinobacterial glucosamine kinases. Structural and biochemical studies on a distinctive kinase from the soil bacterium unveiled its preference for glucosamine and provided structural evidence of a phosphoryl transfer to this substrate. Conservation of glucosamine-contacting residues across a large number of uncharacterized actinobacterial proteins unveiled a specific glucosamine binding sequence motif. This family of kinases and their genetic context may represent the missing link for the incorporation of environmental glucosamine into the antibiotic biosynthesis pathways in and can be explored to enhance antibiotic production. The discovery of novel enzymes involved in antibiotic biosynthesis pathways is currently a topic of utmost importance. The high levels of antibiotic resistance detected worldwide threaten our ability to combat infections and other 20th-century medical achievements, namely, organ transplantation or cancer chemotherapy. We have identified and characterized a unique family of enzymes capable of phosphorylating glucosamine to glucosamine-6-phosphate, a crucial molecule directly involved in the activation of antibiotic production pathways in , nature's main source of antimicrobials. The consensus sequence identified for these glucosamine kinases will help establish a molecular fingerprint to reveal yet-uncharacterized sequences in antibiotic producers, which should have an important impact in biotechnological and biomedical applications, including the enhancement and optimization of antibiotic production. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 467.7 KB | Display | ![]() |
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PDB format | ![]() | 392.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 322 KB | Display | ![]() |
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Full document | ![]() | 330.1 KB | Display | |
Data in XML | ![]() | 32.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6hwkC ![]() 6hwlC ![]() 4o7oS ![]() 4u94S C: citing same article ( S: Starting model for refinement |
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Similar structure data | |
Experimental dataset #1 | Data reference: ![]() |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 48308.703 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: SAMN05414137_114149 / Production host: ![]() ![]() |
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-Non-polymers , 5 types, 480 molecules ![](data/chem/img/MG.gif)
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#2: Chemical | ChemComp-MG / #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-CL / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.19 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 100 mM Bis-Tris pH 6.1, 15% (wt/vol) PEG 3350, 0.2 M MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 16, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 1.979→40.736 Å / Num. obs: 59488 / % possible obs: 98.1 % / Redundancy: 3.5 % / Biso Wilson estimate: 34.2 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.036 / Rrim(I) all: 0.067 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 1.98→2.01 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.908 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2936 / CC1/2: 0.584 / Rpim(I) all: 0.557 / Rrim(I) all: 1.067 / % possible all: 97.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4U94, 4O7O Resolution: 1.979→40.736 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.69
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.979→40.736 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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