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- EMDB-35188: CalA3 complex structure with amidation product -

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Basic information

Entry
Database: EMDB / ID: EMD-35188
TitleCalA3 complex structure with amidation product
Map datapostprocessed map
Sample
  • Organelle or cellular component: an assembly-line polyketide synthase module containing KS-AT-DH-KR domains with amidation product
    • Protein or peptide: Beta-ketoacyl-acyl-carrier-protein synthase I
  • Ligand: 11-oxidanylidene-11-(1~{H}-pyrrol-2-yl)undecanoic acid
  • Ligand: 3-HYDROXYANTHRANILIC ACID
Keywordsmegaenzyme / HYDROLASE / TRANSFERASE
Function / homology
Function and homology information


beta-ketoacyl-[acyl-carrier-protein] synthase I / DIM/DIP cell wall layer assembly / fatty acid synthase activity / 3-oxoacyl-[acyl-carrier-protein] synthase activity / antibiotic biosynthetic process / fatty acid biosynthetic process / plasma membrane / cytoplasm
Similarity search - Function
Polyketide synthase, docking domain / Erythronolide synthase docking domain / : / Polyketide synthase dehydratase N-terminal domain / Polyketide synthase, dehydratase domain / PKS_DH / : / Polyketide synthase dehydratase domain / Polyketide synthase, dehydratase domain superfamily / : ...Polyketide synthase, docking domain / Erythronolide synthase docking domain / : / Polyketide synthase dehydratase N-terminal domain / Polyketide synthase, dehydratase domain / PKS_DH / : / Polyketide synthase dehydratase domain / Polyketide synthase, dehydratase domain superfamily / : / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Polyketide synthase, ketoreductase domain / KR domain / Malonyl-CoA ACP transacylase, ACP-binding / : / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase domain superfamily / Acyl transferase/acyl hydrolase/lysophospholipase / Beta-ketoacyl synthase / PKS_KR / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Polyketide synthase, beta-ketoacyl synthase domain / 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 3882cha (bacteria) / Streptomyces chartreusis NRRL 3882 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.84 Å
AuthorsWang J / Wang Z
Funding support China, 1 items
OrganizationGrant numberCountry
Other government2019YFA0905400 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-
UpdateJul 3, 2024-
Current statusJul 3, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35188.png

Downloads & links

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Map

FileDownload / File: emd_35188.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationpostprocessed map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.89 Å/pix.
x 384 pix.
= 341.76 Å		0.89 Å/pix.
x 384 pix.
= 341.76 Å		0.89 Å/pix.
x 384 pix.
= 341.76 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.89 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0089
Minimum - Maximum-0.019615304 - 0.045925274
Average (Standard dev.)0.000112056325 (±0.0010571657)
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_35188_additional_1.map
Annotationfull map
Projections & Slices
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Slices (1/2)
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Histogram

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Half map: half map 2

Fileemd_35188_half_map_1.map
Annotationhalf map 2
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_35188_half_map_2.map
Annotationhalf map 1
Projections & Slices
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Sample components

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Entire : an assembly-line polyketide synthase module containing KS-AT-DH-K...

EntireName: an assembly-line polyketide synthase module containing KS-AT-DH-KR domains with amidation product
Components
  • Organelle or cellular component: an assembly-line polyketide synthase module containing KS-AT-DH-KR domains with amidation product
    • Protein or peptide: Beta-ketoacyl-acyl-carrier-protein synthase I
  • Ligand: 11-oxidanylidene-11-(1~{H}-pyrrol-2-yl)undecanoic acid
  • Ligand: 3-HYDROXYANTHRANILIC ACID

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Supramolecule #1: an assembly-line polyketide synthase module containing KS-AT-DH-K...

SupramoleculeName: an assembly-line polyketide synthase module containing KS-AT-DH-KR domains with amidation product
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Streptomyces chartreusis NRRL 3882cha (bacteria)
Molecular weightTheoretical: 0.36 kDa/nm

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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

UniProtKB: Beta-ketoacyl-acyl-carrier-protein synthase I

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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: 2 / 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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Macromolecule #3: 3-HYDROXYANTHRANILIC ACID

MacromoleculeName: 3-HYDROXYANTHRANILIC ACID / type: ligand / ID: 3 / Number of copies: 2 / Formula: 3HA
Molecular weightTheoretical: 153.135 Da
Chemical component information

ChemComp-3HA:
3-HYDROXYANTHRANILIC 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

BufferpH: 7.9
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 48.06 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.84 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 223652
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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