2RJ8

B-specific alpha-1,3-galactosyltransferase (GTB) +UDP+ H-antigen disaccharide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

ABO(H) blood group A and B glycosyltransferases recognize substrate via specific conformational changes.

Alfaro, J.A.Zheng, R.B.Persson, M.Letts, J.A.Polakowski, R.Bai, Y.Borisova, S.N.Seto, N.O.Lowary, T.L.Palcic, M.M.Evans, S.V.

(2008) J.Biol.Chem. 283: 10097-10108

  • DOI: 10.1074/jbc.M708669200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The final step in the enzymatic synthesis of the ABO(H) blood group A and B antigens is catalyzed by two closely related glycosyltransferases, an alpha-(1-->3)-N-acetylgalactosaminyltransferase (GTA) and an alpha-(1-->3)-galactosyltransferase (GTB). ...

    The final step in the enzymatic synthesis of the ABO(H) blood group A and B antigens is catalyzed by two closely related glycosyltransferases, an alpha-(1-->3)-N-acetylgalactosaminyltransferase (GTA) and an alpha-(1-->3)-galactosyltransferase (GTB). Of their 354 amino acid residues, GTA and GTB differ by only four "critical" residues. High resolution structures for GTB and the GTA/GTB chimeric enzymes GTB/G176R and GTB/G176R/G235S bound to a panel of donor and acceptor analog substrates reveal "open," "semi-closed," and "closed" conformations as the enzymes go from the unliganded to the liganded states. In the open form the internal polypeptide loop (amino acid residues 177-195) adjacent to the active site in the unliganded or H antigen-bound enzymes is composed of two alpha-helices spanning Arg(180)-Met(186) and Arg(188)-Asp(194), respectively. The semi-closed and closed forms of the enzymes are generated by binding of UDP or of UDP and H antigen analogs, respectively, and show that these helices merge to form a single distorted helical structure with alternating alpha-3(10)-alpha character that partially occludes the active site. The closed form is distinguished from the semi-closed form by the ordering of the final nine C-terminal residues through the formation of hydrogen bonds to both UDP and H antigen analogs. The semi-closed forms for various mutants generally show significantly more disorder than the open forms, whereas the closed forms display little or no disorder depending strongly on the identity of residue 176. Finally, the use of synthetic analogs reveals how H antigen acceptor binding can be critical in stabilizing the closed conformation. These structures demonstrate a delicately balanced substrate recognition mechanism and give insight on critical aspects of donor and acceptor specificity, on the order of substrate binding, and on the requirements for catalysis.


    Organizational Affiliation

    Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glycoprotein-fucosylgalactoside alpha-galactosyltransferase
A
294Homo sapiensMutation(s): 0 
Gene Names: ABO
Find proteins for P16442 (Homo sapiens)
Go to Gene View: ABO
Go to UniProtKB:  P16442
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
BHE
Query on BHE

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Download CCD File 
A
octyl 2-O-(6-deoxy-alpha-L-galactopyranosyl)-beta-D-galactopyranoside
H-antigen acceptor; alpha-L-Fucp-(1,2)-Beta-D-Galp-O(CH2)7CH3
C20 H38 O10
GTTDTLMUWQMDNA-ARNYJBIMSA-N
 Ligand Interaction
UDP
Query on UDP

Download SDF File 
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: 1.69 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.198 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 52.450α = 90.00
b = 149.600β = 90.00
c = 78.740γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
MOLREPphasing
d*TREKdata reduction
d*TREKdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-02-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.2: 2018-03-07
    Type: Data collection