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


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 of 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
    • University of Greifswald: Universitat Greifswald, Institute of Biochemistry, GERMANY.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  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
UniProt
Find proteins for W6TP58 (Pedobacter sp. V48)
Explore W6TP58 
Go to UniProtKB:  W6TP58
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupW6TP58
Sequence Annotations
Expand
  • Reference Sequence
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