[English] 日本語
![](img/lk-miru.gif)
- EMDB-15790: Cryo-EM structure apolipoprotein N-acyltransferase Lnt from E.col... -
+
Open data
-
Basic information
Entry | ![]() | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure apolipoprotein N-acyltransferase Lnt from E.coli in complex with FP3 | |||||||||
![]() | ||||||||||
![]() |
| |||||||||
![]() | Lnt / apolipoprotein N-acyltransferase / bacterial lipoprotein / transferase / cryo-EM | |||||||||
Function / homology | ![]() apolipoprotein N-acyltransferase / N-acyltransferase activity / lipoprotein biosynthetic process / outer membrane-bounded periplasmic space / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.02 Å | |||||||||
![]() | Degtjarik O / Smithers L / Boland C / Caffrey M / Shalev Benami M | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() 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 |
|
-
Structure visualization
Supplemental images |
---|
-
Downloads & links
-EMDB archive
Map data | ![]() | 27.2 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 18.2 KB 18.2 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 8 KB | Display | ![]() |
Images | ![]() | 49.8 KB | ||
Filedesc metadata | ![]() | 5.9 KB | ||
Others | ![]() ![]() ![]() | 26.2 MB 48.9 MB 48.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8b0oMC ![]() 8aq2C ![]() 8aq3C ![]() 8aq4C ![]() 8b0kC ![]() 8b0lC ![]() 8b0mC ![]() 8b0nC ![]() 8b0pC M: atomic model generated by this map C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
EMDB pages | ![]() ![]() |
---|
-
Map
File | ![]() | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 0.826 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Additional map: #1
File | emd_15790_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #1
File | emd_15790_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #2
File | emd_15790_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-
Sample components
-Entire : Apolipoprotein N-acyltransferase
Entire | Name: Apolipoprotein N-acyltransferase |
---|---|
Components |
|
-Supramolecule #1: Apolipoprotein N-acyltransferase
Supramolecule | Name: Apolipoprotein N-acyltransferase / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1 |
---|---|
Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Apolipoprotein N-acyltransferase
Macromolecule | Name: Apolipoprotein N-acyltransferase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: apolipoprotein N-acyltransferase |
---|---|
Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 59.264703 KDa |
Recombinant expression | Organism: ![]() ![]() |
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 ISYEIILGEQ VRDNFRPDTD YLLTISNDAW FGKSIGPWQH FQMARMRALE LARPLLRSTN NGITAVIGPQ GEIQA MIPQ FTREVLTTNV TPTTGLTPYA RTGNWPLWVL TALFGFAAVL MSLRQRRK UniProtKB: Apolipoprotein N-acyltransferase |
-Macromolecule #2: [(2~{R})-3-[(2~{R})-3-[[(2~{R})-1-[[(2~{R})-1-[[(2~{R})-6-[(2-ami...
Macromolecule | Name: [(2~{R})-3-[(2~{R})-3-[[(2~{R})-1-[[(2~{R})-1-[[(2~{R})-6-[(2-aminophenyl)carbonylamino]-1-azanyl-1-oxidanylidene-hexan-2-yl]amino]-3-oxidanyl-1-oxidanylidene-propan-2-yl]amino]-3-oxidanyl-1- ...Name: [(2~{R})-3-[(2~{R})-3-[[(2~{R})-1-[[(2~{R})-1-[[(2~{R})-6-[(2-aminophenyl)carbonylamino]-1-azanyl-1-oxidanylidene-hexan-2-yl]amino]-3-oxidanyl-1-oxidanylidene-propan-2-yl]amino]-3-oxidanyl-1-oxidanylidene-propan-2-yl]amino]-2-(hexadecanoylamino)-3-oxidanylidene-propyl]sulfanyl-2-hexadecanoyloxy-propyl] hexadecanoate type: ligand / ID: 2 / Number of copies: 1 / Formula: OJF |
---|---|
Molecular weight | Theoretical: 1.330926 KDa |
Chemical component information | ![]() ChemComp-OJF: |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | single particle reconstruction |
Aggregation state | particle |
-
Sample preparation
Concentration | 14 mg/mL | ||||||||
---|---|---|---|---|---|---|---|---|---|
Buffer | pH: 6 Component:
| ||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV |
-
Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
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: ![]() |
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 |