3ZGF

Crystal structure of the Fucosylgalactoside alpha N- acetylgalactosaminyltransferase (GTA, cisAB mutant L266G, G268A) in complex with in complex with NPE caged UDP-Gal (P2(1)2(1)2(1) space group)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structures of a Human Blood Group Glycosyltransferase in Complex with a Photo-Activatable Udp-Gal Derivative Reveal Two Different Binding Conformations

Jorgensen, R.Batot, G.Mannerstedt, K.Imberty, A.Breton, C.Hindsgaul, O.Royant, A.Palcic, M.M.

(2014) Acta Crystallogr Sect F Struct Biol Cryst Commun 70: 1015

  • DOI: 10.1107/S2053230X1401259X
  • Primary Citation of Related Structures:  
    3ZGF, 3ZGG

  • PubMed Abstract: 
  • Glycosyltransferases (GTs) catalyse the sequential addition of monosaccharides to specific acceptor molecules and play major roles in key biological processes. GTs are classified into two main families depending on the inverted or retained stereochem ...

    Glycosyltransferases (GTs) catalyse the sequential addition of monosaccharides to specific acceptor molecules and play major roles in key biological processes. GTs are classified into two main families depending on the inverted or retained stereochemistry of the glycosidic bond formed during the reaction. While the mechanism of inverting enzymes is well characterized, the precise nature of retaining GTs is still a matter of much debate. In an attempt to clarify this issue, studies were initiated to identify reaction-intermediate states by using a crystallographic approach based on caged substrates. In this paper, two distinct structures of AA(Gly)B, a dual-specificity blood group synthase, are described in complex with a UDP-galactose derivative in which the O6'' atom is protected by a 2-nitrobenzyl group. The distinct conformations of the caged substrate in both structures of the enzyme illustrate the highly dynamic nature of its active site. An attempt was also made to photolyse the caged compound at low temperature, which unfortunately is not possible without damaging the uracil group as well. These results pave the way for kinetic crystallography experiments aiming at trapping and characterizing reaction-intermediate states in the mechanism of enzymatic glycosyl transfer.


    Organizational Affiliation

    Carlsberg Laboratory, Gamle Carlsberg Vej 10, DK-1799 Copenhagen V, Denmark.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HISTO-BLOOD GROUP ABO SYSTEM TRANSFERASEAB298Homo sapiensMutation(s): 2 
Gene Names: ABO
EC: 2.4.1.37 (PDB Primary Data), 2.4.1.40 (PDB Primary Data)
Find proteins for P16442 (Homo sapiens)
Explore P16442 
Go to UniProtKB:  P16442
NIH Common Fund Data Resources
PHAROS  P16442
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IUG
Query on IUG

Download CCD File 
B
1-(2-NITROPHENYL)ETHYL UDP-GALACTOSE
C22 H30 N3 O19 P2
NGBDXGVIYRIOPC-DZEIOYJHSA-N
 Ligand Interaction
UDP
Query on UDP

Download CCD File 
A
URIDINE-5'-DIPHOSPHATE
C9 H14 N2 O12 P2
XCCTYIAWTASOJW-XVFCMESISA-N
 Ligand Interaction
SO4
Query on SO4

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A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MN
Query on MN

Download CCD File 
A, B
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.183 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.84α = 90
b = 78.45β = 90
c = 155.13γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-01-23
    Type: Initial release
  • Version 1.1: 2014-08-06
    Changes: Database references
  • Version 1.2: 2014-08-13
    Changes: Database references
  • Version 1.3: 2018-01-17
    Changes: Data collection