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- EMDB-19772: Fructose 6-phosphate aldolase (FSA) from Escherichia coli -

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Basic information

Entry
Database: EMDB / ID: EMD-19772
TitleFructose 6-phosphate aldolase (FSA) from Escherichia coli
Map dataFructose 6-phosphate aldolase
Sample
  • Complex: Fructose 6-phosphate aldolase
    • Protein or peptide: Fructose-6-phosphate aldolase 1
Keywordsfructose 6-phosphate aldolase / LYASE
Function / homology
Function and homology information


ketone catabolic process / fructose 6-phosphate aldolase activity / Lyases; Carbon-carbon lyases; Aldehyde-lyases / fructose metabolic process / identical protein binding / cytoplasm
Similarity search - Function
Fructose-6-phosphate aldolase / Transaldolase type 3B/Fructose-6-phosphate aldolase / Transaldolase/Fructose-6-phosphate aldolase, archaeal/bacterial / Transaldolase active site. / Transaldolase, active site / Transaldolase signature 1. / Transaldolase/Fructose-6-phosphate aldolase / Transaldolase/Fructose-6-phosphate aldolase / Aldolase-type TIM barrel
Similarity search - Domain/homology
Fructose-6-phosphate aldolase 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsHebert H / Widersten M
Funding support1 items
OrganizationGrant numberCountry
Other private218-0061
CitationJournal: Structure / Year: 2024
Title: Structure of the iminium reaction intermediate in an engineered aldolase explains the carboligation activity toward arylated ketones and aldehydes.
Authors: Hans Hebert / Eda Sönmez / Pasi Purhonen / Mikael Widersten /
Abstract: Two structures of fructose 6-phosphate aldolase, the wild-type and an engineered variant containing five active-site mutations, have been solved by cryoelectron microscopy (cryo-EM). The engineered ...Two structures of fructose 6-phosphate aldolase, the wild-type and an engineered variant containing five active-site mutations, have been solved by cryoelectron microscopy (cryo-EM). The engineered variant affords production of aldols from aryl substituted ketones and aldehydes. This structure was solved to a resolution of 3.1 Å and contains the critical iminium reaction intermediate trapped in the active site. This provides new information that rationalizes the acquired substrate scope and aids in formulating hypotheses of the chemical mechanism. A Tyr residue (Y131) is positioned for a role as catalytic acid/base during the aldol reaction and the different structures demonstrate mobility of this amino acid residue. Further engineering of this fructose 6-phosphate aldolase (FSA) variant, guided by this new structure, identified additional FSA variants that display improved carboligation activities with 2-hydroxyacetophenone and phenylacetaldehyde.
History
DepositionMar 1, 2024-
Header (metadata) releaseMar 12, 2025-
Map releaseMar 12, 2025-
UpdateSep 24, 2025-
Current statusSep 24, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19772.png

Downloads & links

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Map

FileDownload / File: emd_19772.map.gz / Format: CCP4 / Size: 33.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFructose 6-phosphate aldolase
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 206 pix.
= 170.98 Å		0.83 Å/pix.
x 206 pix.
= 170.98 Å		0.83 Å/pix.
x 206 pix.
= 170.98 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.013
Minimum - Maximum-0.03941633 - 0.06365586
Average (Standard dev.)0.0003096358 (±0.0044157323)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions206206206
Spacing206206206
CellA=B=C: 170.98 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Fructose 6-phosphate aldolase, halfmap1

Fileemd_19772_half_map_1.map
AnnotationFructose 6-phosphate aldolase, halfmap1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Fructose 6-phosphate aldolase, halfmap 2

Fileemd_19772_half_map_2.map
AnnotationFructose 6-phosphate aldolase, halfmap 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Fructose 6-phosphate aldolase

EntireName: Fructose 6-phosphate aldolase
Components
  • Complex: Fructose 6-phosphate aldolase
    • Protein or peptide: Fructose-6-phosphate aldolase 1

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Supramolecule #1: Fructose 6-phosphate aldolase

SupramoleculeName: Fructose 6-phosphate aldolase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: Fructose-6-phosphate aldolase 1

MacromoleculeName: Fructose-6-phosphate aldolase 1 / type: protein_or_peptide / ID: 1
Details: The C-terminal TSHHHHH is a His-tag not observed in the map.
Number of copies: 10 / Enantiomer: LEVO / EC number: Lyases; Carbon-carbon lyases; Aldehyde-lyases
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 23.895672 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MELYLDTSDV VAVKALSRIF PLAGVTTNPS IIAAGKKPLD VVLPQLHEAM GGQGRLFAQV MATTAEGMVN DALKLRSIIA DIVVKVPVT AEGLAAIKML KAEGIPTLGT AVYGAAQGLL SALAGAEYVA PYVNRIDAQG GSGIQTVTDL HQLLKMHAPQ A KVLAASFK ...String:
MELYLDTSDV VAVKALSRIF PLAGVTTNPS IIAAGKKPLD VVLPQLHEAM GGQGRLFAQV MATTAEGMVN DALKLRSIIA DIVVKVPVT AEGLAAIKML KAEGIPTLGT AVYGAAQGLL SALAGAEYVA PYVNRIDAQG GSGIQTVTDL HQLLKMHAPQ A KVLAASFK TPRQALDCLL AGCESITLPL DVAQQMISYP AVDAAVAKFE QDWQGAFGRT SITSHHHHH

UniProtKB: Fructose-6-phosphate aldolase 1

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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

Concentration2.3 mg/mL
BufferpH: 8.35 / Component - Concentration: 40.0 mM / Component - Formula: C6H13NO4 / Component - Name: bicine
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 289 K / Instrument: FEI VITROBOT MARK I

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 9816 / Average exposure time: 2.6 sec. / Average electron dose: 48.64 e/Å2
Details: Images were collected in movie-mode, 45 frames at a dose of 1.08 e-/A2.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 251491
CTF correctionSoftware - Name: CTFFIND / Type: PHASE FLIPPING ONLY
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: D5 (2x5 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 162766
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION
Final 3D classificationNumber classes: 3 / Software - Name: RELION
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

1l6w


Chain - Source name: PDB / Chain - Initial model type: experimental model
DetailsInitial fitting using Chimera and then Phenix
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 190
Output model

PDB-8s7h:
Fructose 6-phosphate aldolase (FSA) from Escherichia coli

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