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Structure paper

TitleStructure snapshots reveal the mechanism of a bacterial membrane lipoprotein -acyltransferase.
Journal, issue, pagesSci Adv, Vol. 9, Issue 26, Page eadf5799, Year 2023
Publish dateJun 30, 2023
AuthorsLuke 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 /
PubMed AbstractBacterial 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.
External linksSci Adv / PubMed:37390210 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution2.395 - 3.13 Å
Structure data

15786

8b0k

EMDB-15786, PDB-8b0k:
Cryo-EM structure of apolipoprotein N-acyltransferase Lnt from E. coli (Apo form)
Method: EM (single particle) / Resolution: 3.0 Å

15787

8b0l

EMDB-15787, PDB-8b0l:
Cryo-EM structure of apolipoprotein N-acyltransferase Lnt from E. coli in complex with PE
Method: EM (single particle) / Resolution: 3.13 Å

15788

8b0m

EMDB-15788, PDB-8b0m:
Cryo-EM structure of apolipoprotein N-acyltransferase Lnt from E. coli in complex with PE (C387S mutant)
Method: EM (single particle) / Resolution: 3.01 Å

15789

8b0n

EMDB-15789, PDB-8b0n:
Cryo-EM structure of apolipoprotein N-acyltransferase Lnt from E. coli in complex with Lyso-PE
Method: EM (single particle) / Resolution: 2.67 Å

15790

8b0o

EMDB-15790, PDB-8b0o:
Cryo-EM structure apolipoprotein N-acyltransferase Lnt from E.coli in complex with FP3
Method: EM (single particle) / Resolution: 3.02 Å

15791

8b0p

EMDB-15791, PDB-8b0p:
Cryo-EM structure of apolipoprotein N-acyltransferase Lnt from E. coli in complex with Pam3
Method: EM (single particle) / Resolution: 2.86 Å

PDB-8aq2:
In meso structure of the membrane integral lipoprotein N-acyltransferase Lnt from P. aeruginosa covalently linked with TITC
Method: X-RAY DIFFRACTION / Resolution: 2.6 Å

PDB-8aq3:
In surfo structure of the membrane integral lipoprotein N-acyltransferase Lnt from E. coli in complex with PE
Method: X-RAY DIFFRACTION / Resolution: 2.395 Å

PDB-8aq4:
In surfo structure of the membrane integral lipoprotein N-acyltransferase Lnt from E. coli in complex with TITC and lyso-PE
Method: X-RAY DIFFRACTION / Resolution: 2.62 Å

Chemicals

ChemComp-OLC:
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate

ChemComp-QGT:
~{N}-tridecylmethanethioamide

ChemComp-FLC:
CITRATE ANION

ChemComp-GOL:
GLYCEROL

ChemComp-HOH:
WATER

ChemComp-6OU:
[(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate / phospholipid*YM

ChemComp-PG5:
1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE

ChemComp-PG6:
1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE

ChemComp-TRS:
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / pH buffer*YM

ChemComp-ACT:
ACETATE ION

ChemComp-LMT:
DODECYL-BETA-D-MALTOSIDE / detergent*YM

ChemComp-CL:
Unknown entry

ChemComp-PTY:
PHOSPHATIDYLETHANOLAMINE / phospholipid*YM

ChemComp-OU9:
[(2~{S})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-oxidanyl-propan-2-yl] (~{Z})-octadec-9-enoate

ChemComp-OJF:
[(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

ChemComp-IG7:
[(2~{S})-3-[(2~{S})-3-azanyl-2-(hexadecanoylamino)-3-oxidanylidene-propyl]sulfanyl-2-hexadecanoyloxy-propyl] hexadecanoate

Source
  • escherichia coli k-12 (bacteria)
  • synthetic construct (others)
  • pseudomonas aeruginosa pao1 (bacteria)
KeywordsTRANSFERASE / Lnt / apolipoprotein N-acyltransferase / Bacterial lipoproteins. / bacterial lipoprotein / cryo-EM

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