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- EMDB-35248: Acyl-ACP synthetase structure bound to MC7-ACP -

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Basic information

Entry
Database: EMDB / ID: EMD-35248
TitleAcyl-ACP synthetase structure bound to MC7-ACP
Map data
Sample
  • Complex: Acyl-ACP Synthetase bound to MC7-ACP
    • Protein or peptide: Acyl-acyl carrier protein synthetase
    • Protein or peptide: Acyl carrier protein
  • Ligand: 7-methoxy-7-oxidanylidene-heptanoic acid
  • Ligand: ADENOSINE MONOPHOSPHATE
  • Ligand: N~3~-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-N-(2-sulfanylethyl)-beta-alaninamide
KeywordsAcyl-ACP synthetase / Tool enzyme / CYTOSOLIC PROTEIN / Ligase / CYTOSOLIC PROTEIN-TRANSPORT PROTEIN complex
Function / homology
Function and homology information


Kdo2-lipid A biosynthetic process / ligase activity, forming carbon-sulfur bonds / lipid A biosynthetic process / acyl binding / acyl carrier activity / membrane / cytosol
Similarity search - Function
: / 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 carrier protein (ACP) / Phosphopantetheine attachment site / Phosphopantetheine attachment site. ...: / 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 carrier protein (ACP) / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain
Similarity search - Domain/homology
Acyl carrier protein / Acyl-acyl carrier protein synthetase
Similarity search - Component
Biological speciesVibrio harveyi (bacteria) / Escherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.51 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
DepositionFeb 3, 2023-
Header (metadata) releaseFeb 7, 2024-
Map releaseFeb 7, 2024-
UpdateJan 22, 2025-
Current statusJan 22, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35248.png

Downloads & links

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Map

FileDownload / File: emd_35248.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
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

Projections

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.014 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-1.7671518 - 3.630784
Average (Standard dev.)0.00023970107 (±0.08904343)
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_35248_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_35248_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Acyl-ACP Synthetase bound to MC7-ACP

EntireName: Acyl-ACP Synthetase bound to MC7-ACP
Components
  • Complex: Acyl-ACP Synthetase bound to MC7-ACP
    • Protein or peptide: Acyl-acyl carrier protein synthetase
    • Protein or peptide: Acyl carrier protein
  • Ligand: 7-methoxy-7-oxidanylidene-heptanoic acid
  • Ligand: ADENOSINE MONOPHOSPHATE
  • Ligand: N~3~-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-N-(2-sulfanylethyl)-beta-alaninamide

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

SupramoleculeName: Acyl-ACP Synthetase bound to MC7-ACP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
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: Acyl carrier protein

MacromoleculeName: Acyl carrier protein / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 8.64546 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSTIEERVKK IIGEQLGVKQ EEVTNNASFV EDLGADSLDT VELVMALEEE FDTEIPDEEA EKITTVQAAI DYINGHQA

UniProtKB: Acyl carrier protein

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Macromolecule #3: 7-methoxy-7-oxidanylidene-heptanoic acid

MacromoleculeName: 7-methoxy-7-oxidanylidene-heptanoic acid / type: ligand / ID: 3 / 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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Macromolecule #4: ADENOSINE MONOPHOSPHATE

MacromoleculeName: ADENOSINE MONOPHOSPHATE / type: ligand / ID: 4 / 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 #5: N~3~-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-N-(2-...

MacromoleculeName: N~3~-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-N-(2-sulfanylethyl)-beta-alaninamide
type: ligand / ID: 5 / Number of copies: 6 / Formula: PN7
Molecular weightTheoretical: 358.348 Da
Chemical component information

ChemComp-PN7:
N~3~-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-N-(2-sulfanylethyl)-beta-alaninamide

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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: 2.51 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 247748
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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