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- EMDB-31203: Pyochelin synthetase, a dimeric nonribosomal peptide synthetase e... -

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Basic information

Entry
Database: EMDB / ID: EMD-31203
TitlePyochelin synthetase, a dimeric nonribosomal peptide synthetase elongation module-condensation
Map dataForBetterIntegrity-ArCP-PCP
Sample
  • Organelle or cellular component: pyochelin synthetase, a dimeric nonribosomal peptide synthetase elongation module
Keywordsnonribosomal peptide synthetase / BIOSYNTHETIC PROTEIN
Function / homology
Function and homology information


L-cysteine-[L-cysteinyl-carrier protein] ligase / 2,3-dihydroxybenzoate-serine ligase activity / enterobactin synthetase complex / enterobactin biosynthetic process / amino acid activation for nonribosomal peptide biosynthetic process / phosphopantetheine binding / cytoplasm
Similarity search - Function
Condensation domain / Condensation domain / Amino acid adenylation domain / ANL, N-terminal domain / AMP-binding, conserved site / Chloramphenicol acetyltransferase-like domain superfamily / Putative AMP-binding domain signature. / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / AMP-dependent synthetase/ligase ...Condensation domain / Condensation domain / Amino acid adenylation domain / ANL, N-terminal domain / AMP-binding, conserved site / Chloramphenicol acetyltransferase-like domain superfamily / Putative AMP-binding domain signature. / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / AMP-dependent synthetase/ligase / AMP-binding enzyme / AMP-binding enzyme, C-terminal domain superfamily / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Pyochelin synthase PchE
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsWang JL / Wang ZJ
Funding support China, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)91753123 China
CitationJournal: Nat Commun / Year: 2022
Title: Catalytic trajectory of a dimeric nonribosomal peptide synthetase subunit with an inserted epimerase domain.
Authors: Jialiang Wang / Dandan Li / Lu Chen / Wei Cao / Liangliang Kong / Wei Zhang / Tristan Croll / Zixin Deng / Jingdan Liang / Zhijun Wang /
Abstract: Nonribosomal 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.
History
DepositionApr 15, 2021-
Header (metadata) releaseDec 15, 2021-
Map releaseDec 15, 2021-
UpdateJul 5, 2023-
Current statusJul 5, 2023Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.008
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.008
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_31203.png

Downloads & links

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Map

FileDownload / File: emd_31203.map.gz / Format: CCP4 / Size: 59.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationForBetterIntegrity-ArCP-PCP
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 250 pix.
= 250. Å		1 Å/pix.
x 250 pix.
= 250. Å		1 Å/pix.
x 250 pix.
= 250. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0055 / Movie #1: 0.008
Minimum - Maximum-0.013256104 - 0.043974973
Average (Standard dev.)0.0001286519 (±0.0021529836)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions250250250
Spacing250250250
CellA=B=C: 250.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z111
M x/y/z250250250
origin x/y/z0.0000.0000.000
length x/y/z250.000250.000250.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS250250250
D min/max/mean-0.0130.0440.000

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Supplemental data

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Sample components

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Entire : pyochelin synthetase, a dimeric nonribosomal peptide synthetase e...

EntireName: pyochelin synthetase, a dimeric nonribosomal peptide synthetase elongation module
Components
  • Organelle or cellular component: pyochelin synthetase, a dimeric nonribosomal peptide synthetase elongation module

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Supramolecule #1: pyochelin synthetase, a dimeric nonribosomal peptide synthetase e...

SupramoleculeName: pyochelin synthetase, a dimeric nonribosomal peptide synthetase elongation module
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 160 kDa/nm

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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: 8
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV
DetailsThis sample was homogenous

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 60.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 13742
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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