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- EMDB-37989: Cryo-EM structure of FpGalactosaminidase from Flavonifractor plau... -

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Basic information

Entry
Database: EMDB / ID: EMD-37989
TitleCryo-EM structure of FpGalactosaminidase from Flavonifractor plautii in apo state
Map data
Sample
  • Organelle or cellular component: FpGalactosaminidase
    • Protein or peptide: Alpha-galactosidase
KeywordsFlavonifractor plautii / A to O type blood / D-(+)-Galactosamine hydrochloride / HYDROLASE
Function / homologyMelibiase / : / alpha-galactosidase / alpha-galactosidase activity / Aldolase-type TIM barrel / Glycoside hydrolase superfamily / Alpha-galactosidase
Function and homology information
Biological speciesFlavonifractor plautii (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.59 Å
AuthorsWu G / Han P / Su C / Zhou M / Luo K
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Exp Hematol Oncol / Year: 2025
Title: Structural basis of FpGalNase and its combination with FpGalNAcDeAc for efficient A-to-O blood group conversion.
Authors: Meiling Zhou / Kaishan Luo / Chao Su / Yan Sun / Zuyan Huang / Shuo Ma / Xun Gao / Jiwei Wang / Chen Zhang / Pengcheng Han / Guoqiu Wu /
Abstract: Transfusion safety and blood typing continue to present significant challenges in clinical practice, including risks of incorrect blood transfusions and blood shortages. One promising solution is the ...Transfusion safety and blood typing continue to present significant challenges in clinical practice, including risks of incorrect blood transfusions and blood shortages. One promising solution is the enzymatic conversion of all red blood cell (RBC) types into universal O-type RBCs. However, the major obstacle to this strategy is the relatively low catalytic efficiency of the enzymes involved. In this study, we investigated two enzymes from Flavonifractor plautii, N-acetylgalactosamine deacetylase (FpGalNAcDeAc) and galactosaminidase (FpGalNase), which demonstrate synergistic activity in efficiently converting A-type RBCs to O-type. We optimized treatment conditions, achieving over 99% conversion in just five minutes using phosphate buffer saline and a 16 nM enzyme concentration. Additionally, we engineered two fusion proteins, FpGalNAcDeAc-FpGalNase and FpGalNase-FpGalNAcDeAc, which showed a 28-fold increase in catalytic efficiency compared to the enzyme mixture. Using cryo-electron microscopy, we resolved the full-length structure of FpGalNase, identifying critical active site residues involved in its catalytic mechanism. This study provides essential structural and biochemical insights for clinical applications in blood group conversion, offering a promising approach for producing universal O-type RBCs.
History
DepositionNov 6, 2023-
Header (metadata) releaseNov 13, 2024-
Map releaseNov 13, 2024-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37989.png

Downloads & links

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Map

FileDownload / File: emd_37989.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 280 pix.
= 238. Å		0.85 Å/pix.
x 280 pix.
= 238. Å		0.85 Å/pix.
x 280 pix.
= 238. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.143
Minimum - Maximum-0.0017455765 - 1.7314585
Average (Standard dev.)0.0009409083 (±0.02243788)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 238.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_37989_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_37989_half_map_2.map
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Sample components

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Entire : FpGalactosaminidase

EntireName: FpGalactosaminidase
Components
  • Organelle or cellular component: FpGalactosaminidase
    • Protein or peptide: Alpha-galactosidase

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Supramolecule #1: FpGalactosaminidase

SupramoleculeName: FpGalactosaminidase / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Flavonifractor plautii (bacteria)

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Macromolecule #1: Alpha-galactosidase

MacromoleculeName: Alpha-galactosidase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Flavonifractor plautii (bacteria)
Molecular weightTheoretical: 72.515055 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: YAIAGNGVRV TYDADGQTIT LYRTEGSGLI QMSKPSPLGG PVVGGQEVQD FSHISCDVEQ STSGVMGSGQ RMTITSQSMS TGLIRTYVL ETSDIEEGVV YTATSYEAGA SDVEVSWFIG SVYELYGAED RIWSYNGGGE GPMHYYDTLQ KIDLTDSGKF S RENKQDDT ...String:
YAIAGNGVRV TYDADGQTIT LYRTEGSGLI QMSKPSPLGG PVVGGQEVQD FSHISCDVEQ STSGVMGSGQ RMTITSQSMS TGLIRTYVL ETSDIEEGVV YTATSYEAGA SDVEVSWFIG SVYELYGAED RIWSYNGGGE GPMHYYDTLQ KIDLTDSGKF S RENKQDDT AASIPVSDIY IADGGITVGD ASATRREVHT PVQETSDSAQ VSIGWPGKVI AAGSVIEIGE SFAVVHPGDY YN GLRGYKN AMDHLGVIMP APGDIPDSSY DLRWESWGWG FNWTIDLIIG KLDELQAAGV KQITLDDGWY TNAGDWALNP EKF PNGASD ALRLTDAIHE HGMTALLWWR PCDGGIDSIL YQQHPEYFVM DADGRPARLP TPGGGTNPSL GYALCPMADG AIAS QVDFV NRAMNDWGFD GFKGDYVWSM PECYNPAHNH ASPEESTEKQ SEIYRVSYEA MVANDPNVFN LLCNCGTPQD YYSLP YMTQ IATADPTSVD QTRRRVKAYK ALMGDYFPVT ADHNNIWYLS AVGTGSVLIE KRDLSGTAKE EYEKWLGIAD TVQLQK GRF IGDLYSYGFD PYETYVVEKD GVMYYAFYKD GSKYSPTGYP DIELKGLDPN KMYRIVDYVN DRVVATNLMG DNAVFNT RF SDYLLVKAVE ISEPDP

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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN 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: 2.0 µm / Nominal defocus min: 1.0 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: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.59 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 673717
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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