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Structure paper

TitleCatalytic trajectory of a dimeric nonribosomal peptide synthetase subunit with an inserted epimerase domain.
Journal, issue, pagesNat Commun, Vol. 13, Issue 1, Page 592, Year 2022
Publish dateFeb 1, 2022
AuthorsJialiang Wang / Dandan Li / Lu Chen / Wei Cao / Liangliang Kong / Wei Zhang / Tristan Croll / Zixin Deng / Jingdan Liang / Zhijun Wang /
PubMed AbstractNonribosomal peptide synthetases (NRPSs) are modular assembly-line megaenzymes that synthesize diverse metabolites with wide-ranging biological activities. The structural dynamics of synthetic ...Nonribosomal peptide synthetases (NRPSs) are modular assembly-line megaenzymes that synthesize diverse metabolites with wide-ranging biological activities. The structural dynamics of synthetic elongation has remained unclear. Here, we present cryo-EM structures of PchE, an NRPS elongation module, in distinct conformations. The domain organization reveals a unique "H"-shaped head-to-tail dimeric architecture. The capture of both aryl and peptidyl carrier protein-tethered substrates and intermediates inside the heterocyclization domain and L-cysteinyl adenylate in the adenylation domain illustrates the catalytic and recognition residues. The multilevel structural transitions guided by the adenylation C-terminal subdomain in combination with the inserted epimerase and the conformational changes of the heterocyclization tunnel are controlled by two residues. Moreover, we visualized the direct structural dynamics of the full catalytic cycle from thiolation to epimerization. This study establishes the catalytic trajectory of PchE and sheds light on the rational re-engineering of domain-inserted dimeric NRPSs for the production of novel pharmaceutical agents.
External linksNat Commun / PubMed:35105906 / PubMed Central
MethodsEM (single particle)
Resolution2.97 - 3.9 Å
Structure data

31198

7emy

EMDB-31198, PDB-7emy:
Pyochelin synthetase, a dimeric nonribosomal peptide synthetase elongation module
Method: EM (single particle) / Resolution: 2.97 Å

31199

7en1

EMDB-31199, PDB-7en1:
Pyochelin synthetase, a dimeric nonribosomal peptide synthetase elongation module-after-condensation
Method: EM (single particle) / Resolution: 3.47 Å

31200

7en2

EMDB-31200, PDB-7en2:
Pyochelin synthetase, a dimeric nonribosomal peptide synthetase elongation module-after-condensation, condensation
Method: EM (single particle) / Resolution: 3.78 Å

EMDB-31201:
Pyochelin synthetase, ArCPdonation
Method: EM (single particle) / Resolution: 3.16 Å

EMDB-31202:
Pyochelin synthetase, a dimeric nonribosomal peptide synthetase elongation module-aftercondensation
Method: EM (single particle) / Resolution: 3.78 Å

EMDB-31203:
Pyochelin synthetase, a dimeric nonribosomal peptide synthetase elongation module-condensation
Method: EM (single particle) / Resolution: 3.9 Å

Chemicals

ChemComp-PNS:
4'-PHOSPHOPANTETHEINE / Phosphopantetheine

ChemComp-SAL:
2-HYDROXYBENZOIC ACID / Salicylic acid

ChemComp-MG:
Unknown entry

ChemComp-AMP:
ADENOSINE MONOPHOSPHATE / AMP*YM / Adenosine monophosphate

ChemComp-CYS:
CYSTEINE / Cysteine

ChemComp-J9F:
(4S)-2-(2-hydroxyphenyl)-4,5-dihydro-1,3-thiazole-4-carboxylic acid

Source
  • pseudomonas aeruginosa pao1 (bacteria)
KeywordsLIGASE / nonribosomal peptide synthetase / BIOSYNTHETIC PROTEIN

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