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- EMDB-35190: Acyl-ACP synthetase structure bound to AMP-MC7 -

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Basic information

Entry
Database: EMDB / ID: EMD-35190
TitleAcyl-ACP synthetase structure bound to AMP-MC7
Map data
Sample
  • Complex: Acyl-ACP Synthetase bound to AMP-MC7
    • Protein or peptide: Acyl-acyl carrier protein synthetase
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE MONOPHOSPHATE
  • Ligand: 7-methoxy-7-oxidanylidene-heptanoic acid
KeywordsAcyl-ACP synthetase / Tool enzyme / CYTOSOLIC PROTEIN
Function / homologyligase activity, forming carbon-sulfur bonds / : / ANL, N-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-dependent synthetase/ligase / AMP-binding enzyme / AMP-binding enzyme, C-terminal domain superfamily / Acyl-acyl carrier protein synthetase
Function and homology information
Biological speciesVibrio harveyi (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.76 Å
AuthorsHuang H / Wang C / Chang S / Cui T / Xu Y / Zhang H / Zhou C / Zhang X / Feng Y
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32125003 China
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: Structure and catalytic mechanism of exogenous fatty acid recycling by AasS, a versatile acyl-ACP synthetase.
Authors: Haomin Huang / Chen Wang / Shenghai Chang / Tao Cui / Yongchang Xu / Man Huang / Huimin Zhang / Chun Zhou / Xing Zhang / Youjun Feng /
Abstract: Fatty acids (FAs) are essential building blocks for all the domains of life, of which bacterial de novo synthesis, called type II FA synthesis (FAS II), is energetically expensive. The recycling of ...Fatty acids (FAs) are essential building blocks for all the domains of life, of which bacterial de novo synthesis, called type II FA synthesis (FAS II), is energetically expensive. The recycling of exogenous FAs (eFAs) partially relieves the FAS II demand and, therefore, compromises the efficacy of FAS II-directed antimicrobials. The versatile acyl-acyl carrier protein (ACP) synthetase, AasS, enables bacterial channeling of diverse eFA nutrients through holo-ACP, an activated form of ACP. However, the molecular mechanism for AasS catalysis is not fully understood. Here we report a series of cryo-electron microscopy structures of AasS from the bioluminescent bacterium Vibrio harveyi to provide insights into the catalytic cycle. AasS forms a ring-shaped hexamer, with each protomer folding into two distinct domains. Biochemical and structural analysis suggests that AasS accommodates distinct eFA substrates and the conserved W230 residue has a gating role. Adenosine triphosphate and Mg binding converts the AasS hexamer to a tetramer, which is likely needed for the acyl adenylate intermediate formation. Afterward, AasS reverts to the hexamer conformation in adaption to acyl-ACP production. The complete landscape for eFA scavenging lays a foundation for exploiting the versatility of AasS in biopharmaceuticals.
History
DepositionJan 21, 2023-
Header (metadata) releaseJan 24, 2024-
Map releaseJan 24, 2024-
UpdateJan 22, 2025-
Current statusJan 22, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35190.png

Downloads & links

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Map

FileDownload / File: emd_35190.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.01 Å/pix.
x 320 pix.
= 324.48 Å		1.01 Å/pix.
x 320 pix.
= 324.48 Å		1.01 Å/pix.
x 320 pix.
= 324.48 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.014 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.52
Minimum - Maximum-2.7324862 - 5.43591
Average (Standard dev.)0.00007444039 (±0.14138104)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 324.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_35190_half_map_1.map
Projections & Slices
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Histogram (log scale)

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Half map: #1

Fileemd_35190_half_map_2.map
Projections & Slices
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Sample components

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Entire : Acyl-ACP Synthetase bound to AMP-MC7

EntireName: Acyl-ACP Synthetase bound to AMP-MC7
Components
  • Complex: Acyl-ACP Synthetase bound to AMP-MC7
    • Protein or peptide: Acyl-acyl carrier protein synthetase
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE MONOPHOSPHATE
  • Ligand: 7-methoxy-7-oxidanylidene-heptanoic acid

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Supramolecule #1: Acyl-ACP Synthetase bound to AMP-MC7

SupramoleculeName: Acyl-ACP Synthetase bound to AMP-MC7 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Vibrio harveyi (bacteria)

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Macromolecule #1: Acyl-acyl carrier protein synthetase

MacromoleculeName: Acyl-acyl carrier protein synthetase / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Vibrio harveyi (bacteria)
Molecular weightTheoretical: 60.496258 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MNQYVNDPSN YQLLIKNLLF SPVAFNPEQE IVYANHRRHS YKTFHDRVRQ FANALTKMGV KKGDTVAVMD YDSHRYLECY FAIPMIGAK LHMINVRLSP EQILYTIDHA EDDIILIHEE FLPILDQIKG RIDTVTRYVV LRDDEECEYE RLLEQESTEY N FPDFDENT ...String:
MNQYVNDPSN YQLLIKNLLF SPVAFNPEQE IVYANHRRHS YKTFHDRVRQ FANALTKMGV KKGDTVAVMD YDSHRYLECY FAIPMIGAK LHMINVRLSP EQILYTIDHA EDDIILIHEE FLPILDQIKG RIDTVTRYVV LRDDEECEYE RLLEQESTEY N FPDFDENT VATTFYTTGT TGFPKGVFFT HRQLVLHTMG ILSTIGTNAS QGRLHQGDIY MPITPMFHVH AWGLPYMATM LG VKQVYPG KYVPDVLLNL IEQEKVTFSH CVPTILHLLL SSPKSKAMDF SGWKVVIGGA ALPKALCKSA LERDIDVFAG YGM SETGPI LSIVQLTPEQ LELDVDQQAE YRSKTGKKVA LVEAYIVDED MNKLPHDGET AGEIVVRAPW LTPNYYKDNK NSKA LWRGG YLHTGDVAHI DDEGFIKITD RVKDMIKISG EWVSSLELED ILHQHQSVSE VAVIGMPHNK WGEVPLALVT LKEDA QVTE KELLGFAKDF INKGILAREA LLLKVKIVDE IAKTSVGKVD KKELRKLHL

UniProtKB: Acyl-acyl carrier protein synthetase

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Macromolecule #2: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 6 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #3: ADENOSINE MONOPHOSPHATE

MacromoleculeName: ADENOSINE MONOPHOSPHATE / type: ligand / ID: 3 / Number of copies: 6 / Formula: AMP
Molecular weightTheoretical: 347.221 Da
Chemical component information

ChemComp-AMP:
ADENOSINE MONOPHOSPHATE / AMP*YM

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Macromolecule #4: 7-methoxy-7-oxidanylidene-heptanoic acid

MacromoleculeName: 7-methoxy-7-oxidanylidene-heptanoic acid / type: ligand / ID: 4 / Number of copies: 6 / Formula: OP3
Molecular weightTheoretical: 174.194 Da
Chemical component information

ChemComp-OP3:
7-methoxy-7-oxidanylidene-heptanoic acid

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
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: 2.76 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 199919
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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