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- PDB-7uch: AprA Methyltransferase 1 - GNAT in complex with Mn2+ , SAM, and D... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7uch | ||||||||||||||||||
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Title | AprA Methyltransferase 1 - GNAT in complex with Mn2+ , SAM, and Di-methyl-malonate | ||||||||||||||||||
![]() | AprA Methyltransferase 1 | ||||||||||||||||||
![]() | TRANSFERASE / polyketide synthase | ||||||||||||||||||
Function / homology | ![]() | ||||||||||||||||||
Biological species | ![]() | ||||||||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||||||||
![]() | Skiba, M.A. / Lao, Y. / Smith, J.L. | ||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural Basis for Control of Methylation Extent in Polyketide Synthase Metal-Dependent C -Methyltransferases. Authors: Lao, Y. / Skiba, M.A. / Chun, S.W. / Narayan, A.R.H. / Smith, J.L. #1: ![]() Title: Biosynthesis of t-Butyl in Apratoxin A: Functional Analysis and Architecture of a PKS Loading Module. Authors: Meredith A Skiba / Andrew P Sikkema / Nathan A Moss / Andrew N Lowell / Min Su / Rebecca M Sturgis / Lena Gerwick / William H Gerwick / David H Sherman / Janet L Smith / ![]() Abstract: The unusual feature of a t-butyl group is found in several marine-derived natural products including apratoxin A, a Sec61 inhibitor produced by the cyanobacterium Moorea bouillonii PNG 5-198. Here, ...The unusual feature of a t-butyl group is found in several marine-derived natural products including apratoxin A, a Sec61 inhibitor produced by the cyanobacterium Moorea bouillonii PNG 5-198. Here, we determine that the apratoxin A t-butyl group is formed as a pivaloyl acyl carrier protein (ACP) by AprA, the polyketide synthase (PKS) loading module of the apratoxin A biosynthetic pathway. AprA contains an inactive "pseudo" GCN5-related N-acetyltransferase domain (ΨGNAT) flanked by two methyltransferase domains (MT1 and MT2) that differ distinctly in sequence. Structural, biochemical, and precursor incorporation studies reveal that MT2 catalyzes unusually coupled decarboxylation and methylation reactions to transform dimethylmalonyl-ACP, the product of MT1, to pivaloyl-ACP. Further, pivaloyl-ACP synthesis is primed by the fatty acid synthase malonyl acyltransferase (FabD), which compensates for the ΨGNAT and provides the initial acyl-transfer step to form AprA malonyl-ACP. Additionally, images of AprA from negative stain electron microscopy reveal multiple conformations that may facilitate the individual catalytic steps of the multienzyme module. | ||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 188.5 KB | Display | ![]() |
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PDB format | ![]() | 115.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 27.6 KB | Display | |
Data in CIF | ![]() | 40.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7uciC ![]() 7uclC ![]() 6b3aS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 74825.836 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 323 molecules ![](data/chem/img/MN.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/MU6.gif)
![](data/chem/img/SAH.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/MU6.gif)
![](data/chem/img/SAH.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-MN / |
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#3: Chemical | ChemComp-GOL / |
#4: Chemical | ChemComp-MU6 / |
#5: Chemical | ChemComp-SAH / |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.37 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 11mg/mL protein in 50mM Tris pH7.4, 50mM NaCl, 10%(V/V) glycerol, 1mM S-adenosyl-L-homocysteine (SAH), and 5mM MnCl2. Well solution: 15% PEG 3350, 0.1M di-methyl-malonate Protein to well solution ratio is 2:2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 9, 2017 |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 2.18→45.23 Å / Num. obs: 38749 / % possible obs: 99.87 % / Redundancy: 10.6 % / Biso Wilson estimate: 33.02 Å2 / CC1/2: 0.995 / CC star: 0.999 / Net I/σ(I): 7.37 |
Reflection shell | Resolution: 2.181→2.259 Å / Mean I/σ(I) obs: 1.18 / Num. unique obs: 3805 / CC1/2: 0.495 / CC star: 0.814 / % possible all: 99.42 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6B3A Resolution: 2.18→45.23 Å / SU ML: 0.3282 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.5831 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.78 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.18→45.23 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.18→2.21 Å
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