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- EMDB-7827: AprA Methyltransferase 1 - GNAT - Methyltransferase 2 tridomain -

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Basic information

Entry
Database: EMDB / ID: EMD-7827
TitleAprA Methyltransferase 1 - GNAT - Methyltransferase 2 tridomain
Map dataAprA Methyltransferase 1 - GNAT - Methyltransferase 2 tridomain
Sample
  • Complex: AprA Polyketide Synthase
    • Protein or peptide: AprA
Biological speciesMoorea bouillonii PNG5-198 (bacteria)
Methodsingle particle reconstruction / negative staining / Resolution: 26.0 Å
AuthorsSu M / Skiba MA / Smith JL
CitationJournal: 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
DepositionApr 25, 2018-
Header (metadata) releaseMay 2, 2018-
Map releaseMay 9, 2018-
UpdateJun 27, 2018-
Current statusJun 27, 2018Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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Structure viewerEM map:
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Supplemental images

emd_7827.png

Downloads & links

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Map

FileDownload / File: emd_7827.map.gz / Format: CCP4 / Size: 2.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAprA Methyltransferase 1 - GNAT - Methyltransferase 2 tridomain
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.32 Å/pix.
x 88 pix.
= 380.16 Å		4.32 Å/pix.
x 88 pix.
= 380.16 Å		4.32 Å/pix.
x 88 pix.
= 380.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.32 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.07703043 - 0.36455867
Average (Standard dev.)0.0005850663 (±0.013672505)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions888888
Spacing888888
CellA=B=C: 380.16 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.324.324.32
M x/y/z888888
origin x/y/z0.0000.0000.000
length x/y/z380.160380.160380.160
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ384384384
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS888888
D min/max/mean-0.0770.3650.001

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Supplemental data

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Sample components

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Entire : AprA Polyketide Synthase

EntireName: AprA Polyketide Synthase
Components
  • Complex: AprA Polyketide Synthase
    • Protein or peptide: AprA

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Supramolecule #1: AprA Polyketide Synthase

SupramoleculeName: AprA Polyketide Synthase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Moorea bouillonii PNG5-198 (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #1: AprA

MacromoleculeName: AprA / type: protein_or_peptide / ID: 1 / Enantiomer: DEXTRO
Source (natural)Organism: Moorea bouillonii PNG5-198 (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MHHHHHHSSG VDLGTENLYF QSNALDKIN RYAHGFVAVP VICACSEAGV FELLSQKKSL KLEEIVEHLA ANSG HLMVA MRLLESLSFL YRSQAEEYIL TEQSQQHQII PKALMSLYKY PFELY LKGE VETGISNWIN CSSRRWDTEN SLLSDLLDGV LLIPLLLELK ...String:
MHHHHHHSSG VDLGTENLYF QSNALDKIN RYAHGFVAVP VICACSEAGV FELLSQKKSL KLEEIVEHLA ANSG HLMVA MRLLESLSFL YRSQAEEYIL TEQSQQHQII PKALMSLYKY PFELY LKGE VETGISNWIN CSSRRWDTEN SLLSDLLDGV LLIPLLLELK KQNLLD ESK KIFNTLTNSL KQELSTLFIN LGWAEEKTEG LYLTDIGRFM RDRSLNL GT TASYAPMLLQ MKELLFGNPQ RVFQRNKTEK ERHVNRTLNV VASGFQHE K FFADTDKIII SIFNQQPIEE QPSYIVDMGC GDGTLLKRIY KIIKQFSAR GKVLTEYPII MVGVDYNQEA LDVTDKNLVD IPHLVIPGDI GAPEKLLEQL KAQGIEPEK VLHIRSFLDH DRPFIAPKNT EIAQARSQLD YQVVDVDREG K LIPPHIAV QSLVEHLERW SSIITRHGLL LLEVHSLTPA VVKKYIDESE SL HFDAYHA FSMQHLVEAD VFLMAAAEVG LFSRKEAFRK YPKTLPLTRI TVN HFEKRK YQIRYATVND IPNLLKCATF NQPVNEPFFQ VLLKQTPTAH LLLE YQGEL VAAIFTETKN SNEVLGIREF LVRTSVENWQ VLAKDLLEFV EQWGV VKPG IKEIEGLLKY HEAISNFQKS KWYQSSVLNK KLIEKITLHE LATLEL CNL MAPEYELEAF AARWLLRVFQ DMGVFLREGE SYQESELVSQ LNISPRY QR LLGALLQILH KRGILKIEKD RVFTLARCKT FALENISSEV SAFYDYFS E KYPAHLSWLT VVKRCLEKYP LILRGEVDVN EVVFTDGDME LFAGLFLGH RVADYFNELL ADGVCWEVEQ RLLEEKRAQP IRILEIGAGT GGVTGILLEK LASHAEQIE FWFTDISSVF TRYGESKFKQ FPWVKYQTFD IEKSLDAQGI K SESFDVVI ANNVLHNTKL IHQTLNNSNS LLNTGGLLAL LEFTQPIDIL LY FGGLLQG FWLFEDPEYR LEVGCLLSIP LWQKVLSDCG FDEIIPLGLP CEM HALSKA RESVIFARKH QVQEKTFSEK IKQNLTEN

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7
StainingType: NEGATIVE / Material: uranyl formate

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Electron microscopy

MicroscopeFEI TECNAI 12
Image recordingFilm or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD

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Image processing

CTF correctionSoftware - Name: RELION (ver. 1.4)
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 26.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 4000
Initial angle assignmentType: COMMON LINE / Software - Name: EMAN2 (ver. 2.1)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 1.4)

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