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- EMDB-35189: CalA3 with hydrolysis product -

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Basic information

Entry
Database: EMDB / ID: EMD-35189
TitleCalA3 with hydrolysis product
Map datapostprocessed map
Sample
  • Cell: CalA3, a polyketide synthase catalyzing C-N bond formation
    • Protein or peptide: Beta-ketoacyl-acyl-carrier-protein synthase I
  • Ligand: 11-oxidanylidene-11-(1~{H}-pyrrol-2-yl)undecanoic acid
Function / homology
Function and homology information


beta-ketoacyl-[acyl-carrier-protein] synthase I / 3-oxoacyl-[acyl-carrier-protein] synthase activity / antibiotic biosynthetic process
Similarity search - Function
Polyketide synthase, docking domain / Erythronolide synthase docking domain / : / : / Polyketide synthase dehydratase domain / Polyketide synthase dehydratase N-terminal domain / PKS_DH / Polyketide synthase, dehydratase domain / Polyketide synthase, dehydratase domain superfamily / Polyketide synthase, ketoreductase domain ...Polyketide synthase, docking domain / Erythronolide synthase docking domain / : / : / Polyketide synthase dehydratase domain / Polyketide synthase dehydratase N-terminal domain / PKS_DH / Polyketide synthase, dehydratase domain / Polyketide synthase, dehydratase domain superfamily / Polyketide synthase, ketoreductase domain / KR domain / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Malonyl-CoA ACP transacylase, ACP-binding / PKS_KR / Acyl transferase domain superfamily / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase/acyl hydrolase/lysophospholipase / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / Thiolase-like / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Beta-ketoacyl-acyl-carrier-protein synthase I
Similarity search - Component
Biological speciesStreptomyces chartreusis NRRL 3882 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.97 Å
AuthorsWang J / Wang Z
Funding support China, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)32270033 China
CitationJournal: Nat Commun / Year: 2023
Title: C-N bond formation by a polyketide synthase.
Authors: Jialiang Wang / Xiaojie Wang / Xixi Li / LiangLiang Kong / Zeqian Du / Dandan Li / Lixia Gou / Hao Wu / Wei Cao / Xiaozheng Wang / Shuangjun Lin / Ting Shi / Zixin Deng / Zhijun Wang / Jingdan Liang /
Abstract: Assembly-line polyketide synthases (PKSs) are molecular factories that produce diverse metabolites with wide-ranging biological activities. PKSs usually work by constructing and modifying the ...Assembly-line polyketide synthases (PKSs) are molecular factories that produce diverse metabolites with wide-ranging biological activities. PKSs usually work by constructing and modifying the polyketide backbone successively. Here, we present the cryo-EM structure of CalA3, a chain release PKS module without an ACP domain, and its structures with amidation or hydrolysis products. The domain organization reveals a unique "∞"-shaped dimeric architecture with five connected domains. The catalytic region tightly contacts the structural region, resulting in two stabilized chambers with nearly perfect symmetry while the N-terminal docking domain is flexible. The structures of the ketosynthase (KS) domain illustrate how the conserved key residues that canonically catalyze C-C bond formation can be tweaked to mediate C-N bond formation, revealing the engineering adaptability of assembly-line polyketide synthases for the production of novel pharmaceutical agents.
History
DepositionJan 21, 2023-
Header (metadata) releaseFeb 22, 2023-
Map releaseFeb 22, 2023-
UpdateApr 19, 2023-
Current statusApr 19, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35189.png

Downloads & links

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Map

FileDownload / File: emd_35189.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationpostprocessed map
Voxel sizeX=Y=Z: 0.89 Å
Density
Contour LevelBy AUTHOR: 0.0078
Minimum - Maximum-0.015045934 - 0.03744029
Average (Standard dev.)8.265911e-05 (±0.00085637206)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 341.76 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: full map

Fileemd_35189_additional_1.map
Annotationfull map
Projections & Slices
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Half map: half map 1

Fileemd_35189_half_map_1.map
Annotationhalf map 1
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_35189_half_map_2.map
Annotationhalf map 2
Projections & Slices
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Sample components

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Entire : CalA3, a polyketide synthase catalyzing C-N bond formation

EntireName: CalA3, a polyketide synthase catalyzing C-N bond formation
Components
  • Cell: CalA3, a polyketide synthase catalyzing C-N bond formation
    • Protein or peptide: Beta-ketoacyl-acyl-carrier-protein synthase I
  • Ligand: 11-oxidanylidene-11-(1~{H}-pyrrol-2-yl)undecanoic acid

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Supramolecule #1: CalA3, a polyketide synthase catalyzing C-N bond formation

SupramoleculeName: CalA3, a polyketide synthase catalyzing C-N bond formation
type: cell / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Streptomyces chartreusis NRRL 3882 (bacteria)

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Macromolecule #1: Beta-ketoacyl-acyl-carrier-protein synthase I

MacromoleculeName: Beta-ketoacyl-acyl-carrier-protein synthase I / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Streptomyces chartreusis NRRL 3882 (bacteria)
Molecular weightTheoretical: 178.383562 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MPDEEKLQKY LRKVTAELQQ ARRRLAAAES QSQEPIAVLG IGCRFPGGVR SPEDLWDLVD SGGDAVGGLP AGRGWQAGSA LDGVNAGFI HGVEEFDPYF FGLDPVEAAA MDPQQRLLLE TTWEAFERAG IDPVAARGSR TAVYAGVQFG GYPLLMREAP P PQVLDHLG ...String:
MPDEEKLQKY LRKVTAELQQ ARRRLAAAES QSQEPIAVLG IGCRFPGGVR SPEDLWDLVD SGGDAVGGLP AGRGWQAGSA LDGVNAGFI HGVEEFDPYF FGLDPVEAAA MDPQQRLLLE TTWEAFERAG IDPVAARGSR TAVYAGVQFG GYPLLMREAP P PQVLDHLG LGNSVGAASG RLAYQFGLLG GAVTVDTQCT SSIVALHLAV KALRNGECAL ALAGGACVMS LPTVLMDFHR RS LLAPDGR SKSFAAAADG VSLAEGAGML LLERLSDARR NGHPVMAVIR GTAINQDGAT NGIISPSGRA QERVIRAALA DGR VTADSV DAVEGHGVGA TLGDGVEVTS LLSTYGQERP AGRPLLLGSV KSNIGHTQTV GAVAGIVKLV MALRNERLPR TVHV DGPTP HADWSSGTVR LLTEPEPWRR GERVRRAGLT CLTLSGTNGH LILEEPPADE PAARPANPER TVPLVLSAKS PTALR EQAE RLRATITAAE PVDVGHSLHT TRSSFRHRAV VLGTGREELA AGLDALAGDR TADGLVRGVA RAQGQTALLF GGAGDG TSG DRPADAEGPR TARGLYEAFP AFAEALDEVT EHLAGLLGPE VRAAVREPGP ACAEPTVVGQ AVAFALNTAL HRLLTAF AV RPDATLGHGA GEVAAAYAAG ALSLADGAAL VTALGRITER VATGPGASVW VRATEDEVRA ALSGSQEQVG AAVAAVDE P GTTVVSGDAG AVARVAAHWR AHGRATGAPR PARLLLSPDD EQAALAELRA IVAGLAFREP EVPLLSTVTG QPVEPAELR SAEHWLDHLR GPTRFLDGVR RLRTDGVTRL VGLDLSGDLT GPAGRSAAGF GEPGRPLLLA SVPGGGRPPG QALLSALGEL HTDGVAIDW SQAFEGRGAR RVDLPTYPYQ KVRCWLVPPE PQVSVVAAPP HPLLGTALDL VDATGQSFTQ QLTPGQVAGV F GQQLYGTP VLPAGARLEW LLAAARHGSP DSAWTLTGIR LPGTVSAASG TPVALQTSRE DSGDGHRVRA FVKGPGTGGG RW AERGGAT VVPAVTRPAP DRVDPESLPE GLAELDVAEV YRRLWRQGSD YAEPLRVLRR VWLGGDEAVA LVGTADVPTG PSG WSRWAA VLEAAVQLAA LSGSGPRTPV SVDRLEVSGP PSEVVWLRVR HGADGAADAV VLSGEGVRLA AVQGLRLRPM AGRE PAGLA EAPLERHEVV WHALAEDGRP GAIGGGTGSW LVFSDDPERA AAWCDELALF GVPAVALAGE DAEGRDGTET VPVGT GDPD VVGKTFAELR ERGVTVAGLL VHDAGDAREP ASGADDPLDA ACRRGGRTLA LVRGFLQEYA EQTPRIVLCS AGAAAG LAG GPPHPAQAPL TALFTSLVWE HPELPCAQVD LDPAEDPPTV VSLLGQVMRL PGAGRLAVRG GRWFEARLER RPAPADR GE RLALRPDATY LVAGGDTRHA AAALEWLAAR GARSVVLAGA ESERGDLAGA RTTGHAGIER LEHVAVDLSS AADVARLA E LCADGRPPLR GVLLLPQPVA GGGLDELDGA RFGAELAGAL RGPVELTRRF TDVGLTGGTD FFVLSTSVVS LPGRAGTVV GSAADAFLTA LARHHRQAGL PVVAAAWGPW LESVDESDEA PAVAFAEAGV YPAPGGEMLD ALLPLPAAGE ADGSGEAGLA RVDWDRYLT AGHRPLPYTV LETRASYDEE KAPGFGQNRM

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Macromolecule #2: 11-oxidanylidene-11-(1~{H}-pyrrol-2-yl)undecanoic acid

MacromoleculeName: 11-oxidanylidene-11-(1~{H}-pyrrol-2-yl)undecanoic acid
type: ligand / ID: 2 / Number of copies: 1 / Formula: ONF
Molecular weightTheoretical: 265.348 Da
Chemical component information

ChemComp-ONF:
11-oxidanylidene-11-(1~{H}-pyrrol-2-yl)undecanoic acid

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration4.5 mg/mL
BufferpH: 7.9
GridModel: C-flat-1.2/1.3 / Material: GOLD
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 48.06 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.97 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 141918
FSC plot (resolution estimation)

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