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- EMDB-36790: the wild-typed alpha-galactosidase 5 -

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Basic information

Entry
Database: EMDB / ID: EMD-36790
Titlethe wild-typed alpha-galactosidase 5
Map dataThis map is the wild type of AGAL5
Sample
  • Complex: Tetramer complex of alpha-galactosidase 5
    • Protein or peptide: Alpha-galactosidase
Keywordsalpha-Galactosidase / HYDROLASE
Function / homology
Function and homology information


alpha-galactosidase / alpha-galactosidase activity / carbohydrate catabolic process
Similarity search - Function
Glycosyl hydrolase family 36, N-terminal / Glycosyl hydrolase family 36, C-terminal / Alpha-galactosidase, N-terminal domain superfamily / Glycosyl hydrolase family 36 C-terminal domain / Glycosyl hydrolase family 36 N-terminal domain / Glycoside hydrolase family 36 / Melibiase / : / Glycoside hydrolase family 27/36, conserved site / Alpha-galactosidase signature. ...Glycosyl hydrolase family 36, N-terminal / Glycosyl hydrolase family 36, C-terminal / Alpha-galactosidase, N-terminal domain superfamily / Glycosyl hydrolase family 36 C-terminal domain / Glycosyl hydrolase family 36 N-terminal domain / Glycoside hydrolase family 36 / Melibiase / : / Glycoside hydrolase family 27/36, conserved site / Alpha-galactosidase signature. / Glycosyl hydrolase, all-beta / Aldolase-type TIM barrel / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Biological speciesBlautia pseudococcoides (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.28 Å
AuthorsLi YW / Ru YX
Funding support China, 1 items
OrganizationGrant numberCountry
Other governmentK22227503 China
CitationJournal: Commun Chem / Year: 2024
Title: Activity-based metaproteomics driven discovery and enzymological characterization of potential α-galactosidases in the mouse gut microbiome.
Authors: Jianbing Jiang / Diana Czuchry / Yanxia Ru / Huipai Peng / Junfeng Shen / Teng Wang / Wenjuan Zhao / Weihua Chen / Sen-Fang Sui / Yaowang Li / Nan Li /
Abstract: The gut microbiota offers an extensive resource of enzymes, but many remain uncharacterized. To distinguish the activities of similar annotated proteins and mine the potentially applicable ones in ...The gut microbiota offers an extensive resource of enzymes, but many remain uncharacterized. To distinguish the activities of similar annotated proteins and mine the potentially applicable ones in the microbiome, we applied an effective Activity-Based Metaproteomics (ABMP) strategy using a specific activity-based probe (ABP) to screen the entire gut microbiome for directly discovering active enzymes and their potential applications, not for exploring host-microbiome interactions. By using an activity-based cyclophellitol aziridine probe specific to α-galactosidases (AGAL), we successfully identified and characterized several gut microbiota enzymes possessing AGAL activities. Cryo-electron microscopy analysis of a newly characterized enzyme (AGLA5) revealed the covalent binding conformations between the AGAL5 active site and the cyclophellitol aziridine ABP, which could provide insights into the enzyme's catalytic mechanism. The four newly characterized AGALs have diverse potential activities, including raffinose family oligosaccharides (RFOs) hydrolysis and enzymatic blood group transformation. Collectively, we present a ABMP platform that facilitates gut microbiota AGALs discovery, biochemical activity annotations and potential industrial or biopharmaceutical applications.
History
DepositionJul 10, 2023-
Header (metadata) releaseJul 17, 2024-
Map releaseJul 17, 2024-
UpdateJun 18, 2025-
Current statusJun 18, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_36790.png

Downloads & links

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Map

FileDownload / File: emd_36790.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis map is the wild type of AGAL5
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.92 Å/pix.
x 200 pix.
= 184. Å		0.92 Å/pix.
x 200 pix.
= 184. Å		0.92 Å/pix.
x 200 pix.
= 184. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.92 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.035
Minimum - Maximum-0.09244491 - 0.16337794
Average (Standard dev.)0.0028004718 (±0.01160617)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 184.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: This is the half map 2

Fileemd_36790_half_map_1.map
AnnotationThis is the half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: This is the half map 1

Fileemd_36790_half_map_2.map
AnnotationThis is the half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Tetramer complex of alpha-galactosidase 5

EntireName: Tetramer complex of alpha-galactosidase 5
Components
  • Complex: Tetramer complex of alpha-galactosidase 5
    • Protein or peptide: Alpha-galactosidase

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Supramolecule #1: Tetramer complex of alpha-galactosidase 5

SupramoleculeName: Tetramer complex of alpha-galactosidase 5 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Blautia pseudococcoides (bacteria)

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Macromolecule #1: Alpha-galactosidase

MacromoleculeName: Alpha-galactosidase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Blautia pseudococcoides (bacteria)
Molecular weightTheoretical: 88.017266 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAVIFHEKTK EFHIFNREVS YLMRIMENGQ LENLYYGKVI RDKEDFGYLH EEAMRSQMSV CIPEPGILSM QYTRQEYPVY GTGDYRSPA LTVLQENGSR LVDFSYVSHE IYKGKKGIPP LPSTYAESED EAETLEVTLH DQVTDTDLVL TYTIYEDYPV I TRNARFEQ ...String:
MAVIFHEKTK EFHIFNREVS YLMRIMENGQ LENLYYGKVI RDKEDFGYLH EEAMRSQMSV CIPEPGILSM QYTRQEYPVY GTGDYRSPA LTVLQENGSR LVDFSYVSHE IYKGKKGIPP LPSTYAESED EAETLEVTLH DQVTDTDLVL TYTIYEDYPV I TRNARFEQ KGEQKIVLER AMSASVEFLD MDYELVQLSG AWSRERYVKN RKLEMGIQSV HSLNGTCGGA EHNPFIALKR PQ TTENQGE VYGFSLVYSG NFLAQAEVST FDMTRVMLGI NPEDFSWELN QGESFQTPEV VMVYSDRGLN KMSQAYHRLY RTR LMRVTW RDKARPILLN NWEATYFDFN EEKILKIAEK AKEAGVELFV LDDGWFGARN DDYRGLGDWY VNLEKLPDGI AGLS RKVEA LGLKFGLWVE LEMVNKDSDL YRAHPDWLIG APDRFESHAR HQHVLDFSRK EVVDYIYKMI AKVLRESSIS YIKWD MNRY MTEPYSRGAD ASQQGKVMHK YILGVYDLYT RLTTEFPEIL FESCASGGAR FDPAMLYFAP QTWTSDDTDA SERTKI QYG TSYVYPVVSM GSHVSAVPNH QMHRMTPIET RANVAYFGTF GYELDLNLLS EAELESVKKQ IAFMKEYREL IQVDGDF YR LLSPFEGNET AWMVVAQDKS RAVAAFYQRM NKVNASWIRF KLQGLDAGTL YEVSCDMAPS ASYDESLAKI YGIQTEEN M VKTYRAYGDE LMQVGIPIDR EDLNKKGGDF ASLLYTLKKV TD

UniProtKB: Alpha-galactosidase

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k 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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 94011
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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