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- PDB-8i4z: CalA3 with hydrolysis product -

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Basic information

Entry
Database: PDB / ID: 8i4z
TitleCalA3 with hydrolysis product
ComponentsBeta-ketoacyl-acyl-carrier-protein synthase I
KeywordsTRANSFERASE / polyketide synthase / BIOSYNTHETIC PROTEIN
Function / homology
Function and homology information


polyketide biosynthetic process / beta-ketoacyl-[acyl-carrier-protein] synthase I / fatty acid synthase activity / 3-oxoacyl-[acyl-carrier-protein] synthase activity / antibiotic biosynthetic process / fatty acid biosynthetic process
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 and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. ...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 and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / Polyketide synthase, dehydratase domain superfamily / 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 / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Acyl transferase/acyl hydrolase/lysophospholipase / PKS_KR / Beta-ketoacyl synthase / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-ONF / Beta-ketoacyl-acyl-carrier-protein synthase I
Similarity search - Component
Biological speciesStreptomyces chartreusis NRRL 3882 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.97 Å
AuthorsWang, J. / Wang, Z.
Funding support China, 1items
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, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 3, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-ketoacyl-acyl-carrier-protein synthase I
B: Beta-ketoacyl-acyl-carrier-protein synthase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)357,0323
Polymers356,7672
Non-polymers2651
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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


Mass: 178383.562 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces chartreusis NRRL 3882 (bacteria)
Gene: SCNRRL3882_6975 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2N9BJK0
#2: Chemical ChemComp-ONF / 11-oxidanylidene-11-(1~{H}-pyrrol-2-yl)undecanoic acid


Mass: 265.348 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23NO3 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: CalA3, a polyketide synthase catalyzing C-N bond formation
Type: CELL / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Streptomyces chartreusis NRRL 3882 (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.9
SpecimenConc.: 4.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid type: C-flat-1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: OTHER / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 48.06 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.97 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 141918 / Symmetry type: POINT

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