4D72

Crystal structure of a family 98 glycoside hydrolase catalytic module (Sp3GH98) in complex with the type 2 blood group A-tetrasaccharide (E558A L19 mutant)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.170 

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Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

Towards Efficient Enzymes for the Generation of Universal Blood Through Structure-Guided Directed Evolution.

Kwan, D.H.Constantinescu, I.Chapanian, R.Higgins, M.A.Koetzler, M.Samain, E.Boraston, A.B.Kizhakkedathu, J.N.Withers, S.G.

(2015) J Am Chem Soc 137: 5695

  • DOI: 10.1021/ja5116088
  • Primary Citation of Related Structures:  
    4D6C, 4D6D, 4D6E, 4D6F, 4D6G, 4D6H, 4D6I, 4D6J, 4D71, 4D72

  • PubMed Abstract: 
  • Blood transfusions are critically important in many medical procedures, but the presence of antigens on red blood cells (RBCs, erythrocytes) means that careful blood-typing must be carried out prior to transfusion to avoid adverse and sometimes fatal reactions following transfusion ...

    Blood transfusions are critically important in many medical procedures, but the presence of antigens on red blood cells (RBCs, erythrocytes) means that careful blood-typing must be carried out prior to transfusion to avoid adverse and sometimes fatal reactions following transfusion. Enzymatic removal of the terminal N-acetylgalactosamine or galactose of A- or B-antigens, respectively, yields universal O-type blood, but is inefficient. Starting with the family 98 glycoside hydrolase from Streptococcus pneumoniae SP3-BS71 (Sp3GH98), which cleaves the entire terminal trisaccharide antigenic determinants of both A- and B-antigens from some of the linkages on RBC surface glycans, through several rounds of evolution, we developed variants with vastly improved activity toward some of the linkages that are resistant to cleavage by the wild-type enzyme. The resulting enzyme effects more complete removal of blood group antigens from cell surfaces, demonstrating the potential for engineering enzymes to generate antigen-null blood from donors of various types.


    Organizational Affiliation

    ⊥Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada V8W 3P6.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GLYCOSIDE HYDROLASEA596Streptococcus pneumoniae SP3-BS71Mutation(s): 4 
EC: 3.2.1.102
UniProt
Find proteins for A0A0H2UKY4 (Streptococcus pneumoniae SP3-BS71)
Explore A0A0H2UKY4 
Go to UniProtKB:  A0A0H2UKY4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H2UKY4
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseB 3N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G61459JW
GlyCosmos:  G61459JW
GlyGen:  G61459JW
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
A2G
Query on A2G

Download Ideal Coordinates CCD File 
C [auth A]2-acetamido-2-deoxy-alpha-D-galactopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-CBQIKETKSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.170 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.25α = 90
b = 154.42β = 90
c = 97.08γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-01-21
    Type: Initial release
  • Version 1.1: 2015-04-29
    Changes: Database references
  • Version 1.2: 2015-05-20
    Changes: Database references
  • Version 1.3: 2017-07-05
    Changes: Data collection
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary