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- EMDB-31199: Pyochelin synthetase, a dimeric nonribosomal peptide synthetase e... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-31199 | |||||||||
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Title | Pyochelin synthetase, a dimeric nonribosomal peptide synthetase elongation module-after-condensation | |||||||||
![]() | PchE-after-condensation | |||||||||
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![]() | nonribosomal peptide synthetase / BIOSYNTHETIC PROTEIN / LIGASE | |||||||||
Function / homology | ![]() L-cysteine-[L-cysteinyl-carrier protein] ligase / 2,3-dihydroxybenzoate-serine ligase activity / enterobactin synthetase complex / enterobactin biosynthetic process / amide biosynthetic process / amino acid activation for nonribosomal peptide biosynthetic process / phosphopantetheine binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.47 Å | |||||||||
![]() | Wang JL / Wang ZJ | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 46.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 20.2 KB 20.2 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 8.5 KB | Display | ![]() |
Images | ![]() | 68.4 KB | ||
Others | ![]() ![]() ![]() | 55.6 MB 46.2 MB 46.2 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7en1MC ![]() 7emyC ![]() 7en2C M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | PchE-after-condensation | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: postprocess
File | emd_31199_additional_1.map | ||||||||||||
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Annotation | postprocess | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half1
File | emd_31199_half_map_1.map | ||||||||||||
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Annotation | half1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half2
File | emd_31199_half_map_2.map | ||||||||||||
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Annotation | half2 | ||||||||||||
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Density Histograms |
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Sample components
-Entire : pyochelin synthetase, a dimeric nonribosomal peptide synthetase e...
Entire | Name: pyochelin synthetase, a dimeric nonribosomal peptide synthetase elongation module |
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Components |
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-Supramolecule #1: pyochelin synthetase, a dimeric nonribosomal peptide synthetase e...
Supramolecule | Name: pyochelin synthetase, a dimeric nonribosomal peptide synthetase elongation module type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 160 kDa/nm |
-Macromolecule #1: Dihydroaeruginoic acid synthetase
Macromolecule | Name: Dihydroaeruginoic acid synthetase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 |
Molecular weight | Theoretical: 158.762641 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MDLPPDSRTA LRDWLTEQLA DLLGEPLADV RALADDDDLL GCGLDSIRLM YLQERLRARG STLDFAQLAQ RPCLGAWLDL LACADRLSA PATVALPTAQ DRDQPFELSS VQQAYWLGRG AGEVLGNVSC HAFLEFRTRD VDPQRLAAAA ECVRQRHPML R ARFLDGRQ ...String: MDLPPDSRTA LRDWLTEQLA DLLGEPLADV RALADDDDLL GCGLDSIRLM YLQERLRARG STLDFAQLAQ RPCLGAWLDL LACADRLSA PATVALPTAQ DRDQPFELSS VQQAYWLGRG AGEVLGNVSC HAFLEFRTRD VDPQRLAAAA ECVRQRHPML R ARFLDGRQ QILPTPPLSC FDLQDWRTLQ VDEAERDWQA LRDWRAHECL AVERGQVFLL GLVRMPGGED RLWLSLDLLA AD VESLRLL LAELGVAYLA PERLAEPPAL HFADYLAHRA AQRAEAAARA RDYWLERLPR LPDAPALPLA CAPESIRQPR TRR LAFQLS AGESRRLERL AAQHGVTLSS VFGCAFALVL ARWSESAEFL LNVPLFDRHA DDPRIGEVIA DFTTLLLLEC RMQA GVSFA EAVKSFQRNL HGAIDHAAFP ALEVLREARR QGQPRSAPVV FASNLGEEGF VPAAFRDAFG DLHDMLSQTP QVWLD HQLY RVGDGILLAW DSVVGLFPEG LPETMFEAYV GLLQRLCDSA WGQPADLPLP WAQQARRALL NGQPACATAR TLHRDF FLR AAEAPDADAL LYRDQRVTRG ELAERALRIA GGLREAGVRP GDAVEVSLPR GPQQVAAVFG VLAAGACYVP LDIDQPP AR RRLIEEAAGV CLAITEEDDP QALPPRLDVQ RLLRGPALAA PVPLAPQASA YVIYTSGSTG VPKGVEVSHA AAINTIDA L LDLLRVNASD RLLAVSALDF DLSVFDLFGG LGAGASLVLP AQEQARDAAA WAEAIQRHAV SLWNSAPALL EMALSLPAS QADYRSLRAV LLSGDWVALD LPGRLRPRCA EGCRLHVLGG ATEAGIWSNL QSVDTVPPHW RSIPYGRPLP GQAYRVVDTH GRDVPDLVV GELWIGGASL ARGYRNDPEL SARRFVHDAQ GRWYRTGDRG RYWGDGTLEF LGRVDQQVKV RGQRIELGEV E AALCAQAG VESACAAVLG GGVASLGAVL VPRLAPRAEG SMDLPAAQPF AGLAEAEAVL TREILGALLE APLELDDGLR RR WLDWLAD SAASALPSLD EALRRLGWQA AGLTAMGNAL RGLLAGEQAP AALLLDPWLA PQAVAARLPD GREALARLLE ALP TPAAGE RLRVAVLDTR AGLWLDQGMA SLLRPGLELT LFERSRVLLD AAATRLPERI VVQALDDGLL PAEHLGRYDR VISF AALHA YEASREGLAL AAALLRPQGR LLLVDLLCES PLALLGAALL DDRPLRLAEL PSLLADLAAA GLAPRCLWRS ERIAL VEAL APGLGLDAAA LQAGLEQRLP QAMRPERLWC LPSLPLNGNG KVDRRRLAES MTRALGECRH EPSAEEPLEA HEQALA ECW EAVLKRPVRR REASFFSLGG DSLLATRLLA GIRERFGVRL GMADFYRQPT LAGLARHLQV QTVEIEETQL EEGVLHH HH HHLPSWSHPQ FEK |
-Macromolecule #2: 4'-PHOSPHOPANTETHEINE
Macromolecule | Name: 4'-PHOSPHOPANTETHEINE / type: ligand / ID: 2 / Number of copies: 2 / Formula: PNS |
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Molecular weight | Theoretical: 358.348 Da |
Chemical component information | ![]() ChemComp-PNS: |
-Macromolecule #3: (4S)-2-(2-hydroxyphenyl)-4,5-dihydro-1,3-thiazole-4-carboxylic acid
Macromolecule | Name: (4S)-2-(2-hydroxyphenyl)-4,5-dihydro-1,3-thiazole-4-carboxylic acid type: ligand / ID: 3 / Number of copies: 1 / Formula: J9F |
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Molecular weight | Theoretical: 223.248 Da |
Chemical component information | ![]() ChemComp-J9F: |
-Macromolecule #4: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #5: ADENOSINE MONOPHOSPHATE
Macromolecule | Name: ADENOSINE MONOPHOSPHATE / type: ligand / ID: 5 / Number of copies: 2 / Formula: AMP |
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Molecular weight | Theoretical: 347.221 Da |
Chemical component information | ![]() ChemComp-AMP: |
-Macromolecule #6: CYSTEINE
Macromolecule | Name: CYSTEINE / type: ligand / ID: 6 / Number of copies: 2 / Formula: CYS |
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Molecular weight | Theoretical: 121.158 Da |
Chemical component information | ![]() ChemComp-BTC: |
-Macromolecule #7: 2-HYDROXYBENZOIC ACID
Macromolecule | Name: 2-HYDROXYBENZOIC ACID / type: ligand / ID: 7 / Number of copies: 1 / Formula: SAL |
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Molecular weight | Theoretical: 138.121 Da |
Chemical component information | ![]() ChemComp-SAL: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 8 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. |
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
Details | This sample was homogenous |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 60.8 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |