3IOJ

Crystal structure of the Fucosylgalactoside alpha N-acetylgalactosaminyltransferase (GTA, cisAB mutant L266G, G268A) in complex with UDP

• PDB DOI: https://doi.org/10.2210/pdb3IOJ/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2009-08-14 Released: 2010-04-07 
• Deposition Author(s): Pesnot, T., Jorgensen, R., Palcic, M.M., Wagner, G.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.193 
• R-Value Work: 0.163 
• R-Value Observed: 0.165 

Starting Model: experimental

Literature

Structural and mechanistic basis for a new mode of glycosyltransferase inhibition.

Pesnot, T., Jorgensen, R., Palcic, M.M., Wagner, G.K.

(2010) Nat Chem Biol 6: 321-323

• PubMed: 20364127 
• DOI: https://doi.org/10.1038/nchembio.343
• Primary Citation of Related Structures:  
  3IOH, 3IOI, 3IOJ


• PubMed Abstract: 
  

  Glycosyltransferases are carbohydrate-active enzymes with essential roles in numerous important biological processes. We have developed a new donor analog for galactosyltransferases that locks a representative target enzyme in a catalytically inactive conformation, thus almost completely abolishing sugar transfer. Results with other galactosyltransferases suggest that this unique mode of glycosyltransferase inhibition may also be generally applicable to other members of this important enzyme family.

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Organizational Affiliation: 

School of Pharmacy, University of East Anglia, Norwich, UK.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 70.79 kDa 
• Atom Count: 5,315 
• Modelled Residue Count: 568 
• Deposited Residue Count: 596 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histo-blood group ABO system transferase	A, B	298	Homo sapiens	Mutation(s): 2  Gene Names: ABO EC: 2.4.1.40 (PDB Primary Data), 2.4.1.37 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P16442 (Homo sapiens) Explore P16442  Go to UniProtKB:  P16442
PHAROS:  P16442

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UDP	D [auth A], J [auth B]	URIDINE-5'-DIPHOSPHATE C9 H14 N2 O12 P2 XCCTYIAWTASOJW-XVFCMESISA-N
SO4	F [auth A], G [auth A], H [auth A], L [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	E [auth A], K [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MN	C [auth A], I [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.193 
• R-Value Work: 0.163 
• R-Value Observed: 0.165 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.45	α = 90
b = 77.536	β = 90
c = 153.605	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-04-07 
Deposition Author(s): Pesnot, T., Jorgensen, R., Palcic, M.M., Wagner, G.K.

Revision History  

• Version 1.0: 2010-04-07
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2014-11-12
  Changes: Structure summary
• Version 1.3: 2017-11-01
  Changes: Refinement description
• Version 1.4: 2021-10-13
  Changes: Data collection, Database references, Derived calculations
• Version 1.5: 2023-09-06
  Changes: Data collection, Refinement description