- EMDB-5662: holo-ACP4-PikAIII/C209A/delta ACP5 (no pentaketide) -
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Open data
ID or keywords:
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Basic information
Entry
Database: EMDB / ID: EMD-5662
Title
holo-ACP4-PikAIII/C209A/delta ACP5 (no pentaketide)
Map data
Reconstruction of the 5th module from the pikromycin biosynthetic pathway (PikAIII) lacking the ACP domain with an N-terminal fusion to the ACP domain from module 4 of the pikromycin pathway (ACP4). The ACP4 domain was phosphopantetheinylated.
Sample
Sample: The 5th module from the pikromycin biosynthetic pathway (PikAIII) lacking the ACP domain with an N-terminal fusion to the ACP domain from module 4 of the pikromycin pathway (ACP4) - the ACP4 domain was phosphopantetheinylated
Protein or peptide: PikAIII
Keywords
Type I polyketide synthase module
Function / homology
Function and homology information
10-deoxymethynolide synthase / narbonolide synthase / macrolide biosynthetic process / DIM/DIP cell wall layer assembly / fatty acid synthase activity / acyltransferase activity, transferring groups other than amino-acyl groups / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / identical protein binding ...10-deoxymethynolide synthase / narbonolide synthase / macrolide biosynthetic process / DIM/DIP cell wall layer assembly / fatty acid synthase activity / acyltransferase activity, transferring groups other than amino-acyl groups / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / identical protein binding / plasma membrane / cytoplasm Similarity search - Function
Journal: Nature / Year: 2014 Title: Structure of a modular polyketide synthase. Authors: Somnath Dutta / Jonathan R Whicher / Douglas A Hansen / Wendi A Hale / Joseph A Chemler / Grady R Congdon / Alison R H Narayan / Kristina Håkansson / David H Sherman / Janet L Smith / Georgios Skiniotis / Abstract: Polyketide natural products constitute a broad class of compounds with diverse structural features and biological activities. Their biosynthetic machinery, represented by type I polyketide synthases ...Polyketide natural products constitute a broad class of compounds with diverse structural features and biological activities. Their biosynthetic machinery, represented by type I polyketide synthases (PKSs), has an architecture in which successive modules catalyse two-carbon linear extensions and keto-group processing reactions on intermediates covalently tethered to carrier domains. Here we used electron cryo-microscopy to determine sub-nanometre-resolution three-dimensional reconstructions of a full-length PKS module from the bacterium Streptomyces venezuelae that revealed an unexpectedly different architecture compared to the homologous dimeric mammalian fatty acid synthase. A single reaction chamber provides access to all catalytic sites for the intramodule carrier domain. In contrast, the carrier from the preceding module uses a separate entrance outside the reaction chamber to deliver the upstream polyketide intermediate for subsequent extension and modification. This study reveals for the first time, to our knowledge, the structural basis for both intramodule and intermodule substrate transfer in polyketide synthases, and establishes a new model for molecular dissection of these multifunctional enzyme systems.
History
Deposition
May 2, 2013
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Header (metadata) release
Jul 3, 2013
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Map release
Jun 25, 2014
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Update
Oct 22, 2014
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Current status
Oct 22, 2014
Processing site: RCSB / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
Download / File: emd_5662.map.gz / Format: CCP4 / Size: 26.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation
Reconstruction of the 5th module from the pikromycin biosynthetic pathway (PikAIII) lacking the ACP domain with an N-terminal fusion to the ACP domain from module 4 of the pikromycin pathway (ACP4). The ACP4 domain was phosphopantetheinylated.
Voxel size
X=Y=Z: 2.24 Å
Density
Contour Level
By AUTHOR: 6.2 / Movie #1: 6.2
Minimum - Maximum
-9.81426525 - 29.80714798
Average (Standard dev.)
0.0 (±1.0)
Symmetry
Space group: 1
Details
EMDB XML:
Map geometry
Axis order
X
Y
Z
Origin
-36
-36
-36
Dimensions
192
192
192
Spacing
192
192
192
Cell
A=B=C: 430.08002 Å α=β=γ: 90.0 °
CCP4 map header:
mode
Image stored as Reals
Å/pix. X/Y/Z
2.24
2.24
2.24
M x/y/z
192
192
192
origin x/y/z
0.000
0.000
0.000
length x/y/z
430.080
430.080
430.080
α/β/γ
90.000
90.000
90.000
start NX/NY/NZ
-132
-122
-147
NX/NY/NZ
250
274
261
MAP C/R/S
1
2
3
start NC/NR/NS
-36
-36
-36
NC/NR/NS
192
192
192
D min/max/mean
-9.814
29.807
0.000
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Supplemental data
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Sample components
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Entire : The 5th module from the pikromycin biosynthetic pathway (PikAIII)...
Entire
Name: The 5th module from the pikromycin biosynthetic pathway (PikAIII) lacking the ACP domain with an N-terminal fusion to the ACP domain from module 4 of the pikromycin pathway (ACP4) - the ACP4 ...Name: The 5th module from the pikromycin biosynthetic pathway (PikAIII) lacking the ACP domain with an N-terminal fusion to the ACP domain from module 4 of the pikromycin pathway (ACP4) - the ACP4 domain was phosphopantetheinylated
Components
Sample: The 5th module from the pikromycin biosynthetic pathway (PikAIII) lacking the ACP domain with an N-terminal fusion to the ACP domain from module 4 of the pikromycin pathway (ACP4) - the ACP4 domain was phosphopantetheinylated
Protein or peptide: PikAIII
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Supramolecule #1000: The 5th module from the pikromycin biosynthetic pathway (PikAIII)...
Supramolecule
Name: The 5th module from the pikromycin biosynthetic pathway (PikAIII) lacking the ACP domain with an N-terminal fusion to the ACP domain from module 4 of the pikromycin pathway (ACP4) - the ACP4 ...Name: The 5th module from the pikromycin biosynthetic pathway (PikAIII) lacking the ACP domain with an N-terminal fusion to the ACP domain from module 4 of the pikromycin pathway (ACP4) - the ACP4 domain was phosphopantetheinylated type: sample / ID: 1000 Details: Sample was not frozen prior to loading on the grid. The sample was monodisperse. Oligomeric state: Dimer / Number unique components: 1
Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 89 K / Instrument: FEI VITROBOT MARK IV / Method: Blot for 1.5-2.0 seconds before plunging.
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Electron microscopy
Microscope
FEI TECNAI F20
Temperature
Min: 89 K / Max: 89 K
Alignment procedure
Legacy - Astigmatism: Objective lens astigmatism was corrected at 135,000 times magnification
Date
Jan 1, 2013
Image recording
Category: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 90 / Average electron dose: 20 e/Å2
Electron beam
Acceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN
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