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: 1.701 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.182 

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 70: 1015

  • DOI: 10.1107/S2053230X1401259X
  • Primary Citation of Related Structures:  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

    Department of Microbiology and Infection Control, Statens Serum Institut, 5 Artillerivej, DK-2300 Copenhagen S, Denmark.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HISTO-BLOOD GROUP ABO SYSTEM TRANSFERASE
A, B
298Homo sapiensGene Names: ABO
EC: 2.4.1.37, 2.4.1.40
Find proteins for P16442 (Homo sapiens)
Go to Gene View: ABO
Go to UniProtKB:  P16442
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

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Download CCD File 
A, B
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
IUG
Query on IUG

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Download CCD File 
B
1-(2-NITROPHENYL)ETHYL UDP-GALACTOSE
C22 H30 N3 O19 P2
NGBDXGVIYRIOPC-DZEIOYJHSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
UDP
Query on UDP

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Download CCD File 
A
URIDINE-5'-DIPHOSPHATE
C9 H14 N2 O12 P2
XCCTYIAWTASOJW-XVFCMESISA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.701 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.182 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 52.840α = 90.00
b = 78.450β = 90.00
c = 155.130γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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