Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 69.89 kDa 
• Atom Count: 5683 
• Modelled Residue Count: 586 
• Deposited Residue Count: 596 
• Unique protein chains: 1

4D71

Crystal structure of a family 98 glycoside hydrolase catalytic module (Sp3GH98) in complex with the type 2 blood group A-tetrasaccharide (E558A X02 mutant)

• PDB DOI: 10.2210/pdb4D71/pdb

• Classification: HYDROLASE
• Organism(s): Streptococcus pneumoniae SP3-BS71
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2014-11-19 Released: 2015-01-21 
• Deposition Author(s): Kwan, D.H., Constantinescu, I., Chapanian, R., Higgins, M.A., Samain, E., Boraston, A.B., Kizhakkedathu, J.N., Withers, S.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free: 0.201 
• R-Value Work: 0.163 
• R-Value Observed: 0.165 

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

• PubMed: 25870881 
• 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. 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GLYCOSIDE HYDROLASE	A	596	Streptococcus pneumoniae SP3-BS71	Mutation(s): 3  EC: 3.2.1.102
UniProt
Find proteins for A0A0H2UKY3 (Streptococcus pneumoniae SP3-BS71) Explore A0A0H2UKY3  Go to UniProtKB:  A0A0H2UKY3

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-L-fucopyranose-(1-2)-[2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)]beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	4		N/A
Glycosylation Resources
GlyTouCan:  G74353FF GlyCosmos:  G74353FF GlyGen:  G74353FF

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A], E [auth A], F [auth A], G [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free: 0.201 
• R-Value Work: 0.163 
• R-Value Observed: 0.165 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.33	α = 90
b = 155.02	β = 90
c = 97.26	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-11-19 
• Released Date: 2015-01-21 
Deposition Author(s): Kwan, D.H., Constantinescu, I., Chapanian, R., Higgins, M.A., Samain, E., Boraston, A.B., Kizhakkedathu, J.N., Withers, S.G.

Revision History  

• 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