9I4F | pdb_00009i4f

Blood Type B-converting alpha-1,3-galactosidase PpaGal from Pedobacter panaciterrae in its apo form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 
    0.285 (Depositor), 0.278 (DCC) 
  • R-Value Work: 
    0.251 (Depositor), 0.240 (DCC) 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Validation slider image for 9I4F

This is version 1.2 of the entry. See complete history

Literature

Identification and Protein Engineering of Galactosidases for the Conversion of Blood Type B to Blood Type O.

Moller, C.Terholsen, H.Schmoker, O.Le, T.L.A.Wesche, J.Schmiade, P.Eppendorfer, E.Rimkus, N.Girbardt, B.Bottcher, D.Palm, G.J.Hoppen, J.Lammers, M.Greinacher, A.Aurich, K.Bornscheuer, U.T.

(2025) Chembiochem 26: e202500072-e202500072

  • DOI: https://doi.org/10.1002/cbic.202500072
  • Primary Citation Related Structures: 
    9I4F, 9I4G

  • PubMed Abstract: 

    The supply of blood products such as red blood cells poses a challenge due to rising demand and declining donor numbers. Careful matching of blood products of different types is required. Only type O of the blood types A, B, AB and O can be received by any patient without transfusion incompatibilities. Therefore, O-type blood can be considered "universal blood" and is especially needed in emergency situations. In this study, we focused on the conversion of the B antigen by enzymatic deglycosylation to generate the H antigen determining O-type blood. For this, we characterized several previously unstudied α-1,3-galactosidases belonging to the GH110 family. Our findings revealed that the α-1,3-galactosidase from Pedobacter panaciterrae (PpaGal) exhibits superior efficiency compared to previously described galactosidases. We further increased the activity of PpaGal by 2.5-fold using site-directed mutagenesis. Moreover, we solved two crystal structures of PpaGal, one in the apo-state and another in complex with d-galactose. The combination of our mutagenesis study with the solved crystal structures provides valuable information to guide further optimization of PpaGal or other B antigen converting enzymes paving the way for the easier production of universal blood from B-type blood.


  • Organizational Affiliation
    • Institute of Biochemistry, Department of Biotechnology and Enzyme Catalysis, University Greifswald, Felix-Hausdorff-Straße 4, 17487, Greifswald, Germany.

Macromolecule Content 

  • Total Structure Weight: 263.5 kDa 
  • Atom Count: 18,622 
  • Modeled Residue Count: 2,336 
  • Deposited Residue Count: 2,336 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Alpha-1,3-galactosidase PpaGal
A, B, C, D
584Pedobacter panaciterraeMutation(s): 0 
EC: 3.2.1.22

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EDO

Query on EDO



Download:Ideal Coordinates CCD File
E [auth B]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free:  0.285 (Depositor), 0.278 (DCC) 
  • R-Value Work:  0.251 (Depositor), 0.240 (DCC) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.13α = 90
b = 129.026β = 90.177
c = 108.296γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Cootmodel building
PHASERphasing
XDSdata scaling
XDSdata reduction
MxCuBEdata collection

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)Germany443535983

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-12
    Type: Initial release
  • Version 1.1: 2025-03-19
    Changes: Database references
  • Version 1.2: 2025-04-30
    Changes: Database references