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Yorodumi- EMDB-15791: Cryo-EM structure of apolipoprotein N-acyltransferase Lnt from E.... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15791 | |||||||||
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Title | Cryo-EM structure of apolipoprotein N-acyltransferase Lnt from E. coli in complex with Pam3 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Lnt / apolipoprotein N-acyltransferase / bacterial lipoprotein / transferase / cryo-EM | |||||||||
Function / homology | Function and homology information apolipoprotein N-acyltransferase / N-acyltransferase activity / lipoprotein biosynthetic process / outer membrane-bounded periplasmic space / plasma membrane Similarity search - Function | |||||||||
Biological species | Escherichia coli K-12 (bacteria) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.86 Å | |||||||||
Authors | Degtjarik O / Smithers L / Boland C / Caffrey M / Shalev Benami M | |||||||||
Funding support | Ireland, 2 items
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Citation | Journal: Sci Adv / Year: 2023 Title: Structure snapshots reveal the mechanism of a bacterial membrane lipoprotein -acyltransferase. Authors: Luke Smithers / Oksana Degtjarik / Dietmar Weichert / Chia-Ying Huang / Coilín Boland / Katherine Bowen / Abraham Oluwole / Corinne Lutomski / Carol V Robinson / Eoin M Scanlan / Meitian ...Authors: Luke Smithers / Oksana Degtjarik / Dietmar Weichert / Chia-Ying Huang / Coilín Boland / Katherine Bowen / Abraham Oluwole / Corinne Lutomski / Carol V Robinson / Eoin M Scanlan / Meitian Wang / Vincent Olieric / Moran Shalev-Benami / Martin Caffrey / Abstract: Bacterial lipoproteins (BLPs) decorate the surface of membranes in the cell envelope. They function in membrane assembly and stability, as enzymes, and in transport. The final enzyme in the BLP ...Bacterial lipoproteins (BLPs) decorate the surface of membranes in the cell envelope. They function in membrane assembly and stability, as enzymes, and in transport. The final enzyme in the BLP synthesis pathway is the apolipoprotein -acyltransferase, Lnt, which is proposed to act by a ping-pong mechanism. Here, we use x-ray crystallography and cryo-electron microscopy to chart the structural changes undergone during the progress of the enzyme through the reaction. We identify a single active site that has evolved to bind, individually and sequentially, substrates that satisfy structural and chemical criteria to position reactive parts next to the catalytic triad for reaction. This study validates the ping-pong mechanism, explains the molecular bases for Lnt's substrate promiscuity, and should facilitate the design of antibiotics with minimal off-target effects. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_15791.map.gz | 27.3 MB | EMDB map data format | |
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Header (meta data) | emd-15791-v30.xml emd-15791.xml | 18.8 KB 18.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_15791_fsc.xml | 8 KB | Display | FSC data file |
Images | emd_15791.png | 48.7 KB | ||
Others | emd_15791_additional_1.map.gz emd_15791_half_map_1.map.gz emd_15791_half_map_2.map.gz | 26.2 MB 48.9 MB 48.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15791 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15791 | HTTPS FTP |
-Validation report
Summary document | emd_15791_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
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Full document | emd_15791_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | emd_15791_validation.xml.gz | 15.7 KB | Display | |
Data in CIF | emd_15791_validation.cif.gz | 19.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15791 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15791 | HTTPS FTP |
-Related structure data
Related structure data | 8b0pMC 8aq2C 8aq3C 8aq4C 8b0kC 8b0lC 8b0mC 8b0nC 8b0oC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_15791.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.826 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: #1
File | emd_15791_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_15791_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_15791_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Apolipoprotein N-acyltransferase
Entire | Name: Apolipoprotein N-acyltransferase |
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Components |
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-Supramolecule #1: Apolipoprotein N-acyltransferase
Supramolecule | Name: Apolipoprotein N-acyltransferase / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Escherichia coli K-12 (bacteria) |
-Macromolecule #1: Apolipoprotein N-acyltransferase
Macromolecule | Name: Apolipoprotein N-acyltransferase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO EC number: Transferases; Acyltransferases; Transferring groups other than aminoacyl groups |
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Source (natural) | Organism: Escherichia coli K-12 (bacteria) / Strain: K12 |
Molecular weight | Theoretical: 59.248695 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MGSSHHHHHH SSGLVPRGSH MAFASLIERQ RIRLLLALLF GACGTLAFSP YDVWPAAIIS LMGLQALTFN RRPLQSAAIG FCWGFGLFG SGINWVYVSI ATFGGMPGPV NIFLVVLLAA YLSLYTGLFA GVLSRLWPKT TWLRVAIAAP ALWQVTEFLR G WVLTGFPW ...String: MGSSHHHHHH SSGLVPRGSH MAFASLIERQ RIRLLLALLF GACGTLAFSP YDVWPAAIIS LMGLQALTFN RRPLQSAAIG FCWGFGLFG SGINWVYVSI ATFGGMPGPV NIFLVVLLAA YLSLYTGLFA GVLSRLWPKT TWLRVAIAAP ALWQVTEFLR G WVLTGFPW LQFGYSQIDG PLKGLAPIMG VEAINFLLMM VSGLLALALV KRNWRPLVVA VVLFALPFPL RYIQWFTPQP EK TIQVSMV QGDIPQSLKW DEGQLLNTLK IYYNATAPLM GKSSLIIWPE SAITDLEINQ QPFLKALDGE LRDKGSSLVT GIV DARLNK QNRYDTYNTI ITLGKGAPYS YESADRYNKN HLVPFGEFVP LESILRPLAP FFDLPMSSFS RGPYIQPPLS ANGI ELTAA IAYEIILGEQ VRDNFRPDTD YLLTISNDAW FGKSIGPWQH FQMARMRALE LARPLLRSTN NGITAVIGPQ GEIQA MIPQ FTREVLTTNV TPTTGLTPYA RTGNWPLWVL TALFGFAAVL MSLRQRRK |
-Macromolecule #2: Pam3-SKKKK
Macromolecule | Name: Pam3-SKKKK / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 621.812 Da |
Sequence | String: SKKKK |
-Macromolecule #3: [(2~{S})-3-[(2~{S})-3-azanyl-2-(hexadecanoylamino)-3-oxidanyliden...
Macromolecule | Name: [(2~{S})-3-[(2~{S})-3-azanyl-2-(hexadecanoylamino)-3-oxidanylidene-propyl]sulfanyl-2-hexadecanoyloxy-propyl] hexadecanoate type: ligand / ID: 3 / Number of copies: 1 / Formula: IG7 |
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Molecular weight | Theoretical: 909.478 Da |
Chemical component information | ChemComp-IG7: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 14 mg/mL | ||||||||
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Buffer | pH: 6 Component:
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 33.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |