+Open data
-Basic information
Entry | Database: PDB / ID: 6d6y | ||||||||||||
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Title | AprA Methyltransferase 2 - GNAT didomain in complex with SAH | ||||||||||||
Components | AprA Methyltransferase 2 | ||||||||||||
Keywords | TRANSFERASE / methyltransferase / decarboxylase / apratoxin / GCN5 related N-acetyltransferase | ||||||||||||
Function / homology | Function and homology information | ||||||||||||
Biological species | Moorea bouillonii (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.246 Å | ||||||||||||
Authors | Sikkema, A.P. / Smith, J.L. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: ACS Chem Biol / Year: 2018 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6d6y.cif.gz | 229.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6d6y.ent.gz | 181 KB | Display | PDB format |
PDBx/mmJSON format | 6d6y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d6/6d6y ftp://data.pdbj.org/pub/pdb/validation_reports/d6/6d6y | HTTPS FTP |
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-Related structure data
Related structure data | 7827C 2reeS 5thyS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 60130.934 Da / Num. of mol.: 1 / Fragment: GNAT didomain (UNP residues 503-1022) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Moorea bouillonii (bacteria) / Gene: BJP37_16135 / Plasmid: pMCSG7 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A1U7N2Z8, Transferases; Transferring one-carbon groups; Methyltransferases |
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#2: Chemical | ChemComp-TMO / |
#3: Chemical | ChemComp-SAH / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.75 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.01-0.05 M trimethylamine N-oxide, 12-17% PEG8000, 0.12 M Tris, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 9, 2016 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.246→48.861 Å / Num. obs: 60876 / % possible obs: 98.4 % / Redundancy: 6.067 % / Biso Wilson estimate: 52.96 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.09 / Rrim(I) all: 0.099 / Χ2: 1.039 / Net I/σ(I): 12.09 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 5THY & 2REE Resolution: 2.246→48.861 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.51
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 179.05 Å2 / Biso mean: 68.1807 Å2 / Biso min: 29.4 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.246→48.861 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22
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