2WNF | pdb_00002wnf

Crystal Structure of a Mammalian Sialyltransferase in complex with Gal-beta-1-3GalNAc-ortho-nitrophenol

• PDB DOI: https://doi.org/10.2210/pdb2WNF/pdb

• Classification: TRANSFERASE
• Organism(s): Sus scrofa
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-07-09 Released: 2009-10-13 
• Deposition Author(s): Rao, F.V., Rich, J.R., Raikic, B., Wakarchuk, W.W., Withers, S.G., Strynadka, N.C.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free: 
  0.195 (Depositor), 0.314 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.307 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

Literature

Structural Insight Into Mammalian Sialyltransferases.

Rao, F.V., Rich, J.R., Rakic, B., Buddai, S., Schwartz, M.F., Johnson, K., Bowe, C., Wakarchuk, W.W., Defrees, S., Withers, S.G., Strynadka, N.C.J.

(2009) Nat Struct Mol Biol 16: 1186

• PubMed: 19820709 
• DOI: https://doi.org/10.1038/nsmb.1685
• Primary Citation Related Structures: 
  2WML, 2WNB, 2WNF


• PubMed Abstract: 
  

  Mammalian cell surfaces are modified by complex arrays of glycoproteins, glycolipids and polysaccharides, many of which terminate in sialic acid and have central roles in essential processes including cell recognition, adhesion and immunogenicity. Sialylation of glycoconjugates is performed by a set of sequence-related enzymes known as sialyltransferases (STs). Here we present the crystal structure of a mammalian ST, porcine ST3Gal-I, providing a structural basis for understanding the mechanism and specificity of these enzymes and for the design of selective inhibitors.

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Organizational Affiliation: 
• Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, Canada.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 35.27 kDa 
• Atom Count: 2,699 
• Modeled Residue Count: 272 
• Deposited Residue Count: 298 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CMP-N-ACETYLNEURAMINATE-BETA-GALACTOSAMIDE-ALPHA-2,3-SIALYLTRANSFERASE	A	298	Sus scrofa	Mutation(s): 0  EC: 2.4.99.4 (PDB Primary Data), 2.4.3.4 (UniProt), 2.4.3.2 (UniProt)
UniProt
Find proteins for Q02745 (Sus scrofa) Explore Q02745  Go to UniProtKB:  Q02745

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-alpha-D-galactopyranose	B	2		N/A
Glycosylation Resources
GlyTouCan: G00031MO GlyCosmos: G00031MO GlyGen: G00031MO

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OPO	C [auth A]	O-NITROPHENOL C6 H5 N O3 IQUPABOKLQSFBK-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900084	B	Thomsen-Friedenreich antigen	Oligosaccharide / Antigen

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free:  0.195 (Depositor), 0.314 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.307 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.987	α = 90
b = 78.347	β = 90
c = 99.191	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-10-13 
Deposition Author(s): Rao, F.V., Rich, J.R., Raikic, B., Wakarchuk, W.W., Withers, S.G., Strynadka, N.C.J.

Revision History  

• Version 1.0: 2009-10-13
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2011-11-16
  Changes: Database references, Other
• Version 1.3: 2015-05-20
  Changes: Refinement description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary
• Version 2.1: 2023-12-13
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-10-23
  Changes: Structure summary
• Version 3.0: 2026-04-15
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary