5C3B

Crystal structure of ABBA + UDP-C-Gal (long soak) + DI


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

High Resolution Structures of the Human ABO(H) Blood Group Enzymes in Complex with Donor Analogs Reveal That the Enzymes Utilize Multiple Donor Conformations to Bind Substrates in a Stepwise Manner.

Gagnon, S.M.Meloncelli, P.J.Zheng, R.B.Haji-Ghassemi, O.Johal, A.R.Borisova, S.N.Lowary, T.L.Evans, S.V.

(2015) J.Biol.Chem. 290: 27040-27052

  • DOI: 10.1074/jbc.M115.682401
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Homologous glycosyltransferases α-(1→3)-N-acetylgalactosaminyltransferase (GTA) and α-(1→3)-galactosyltransferase (GTB) catalyze the final step in ABO(H) blood group A and B antigen synthesis through sugar transfer from activated donor to the H antig ...

    Homologous glycosyltransferases α-(1→3)-N-acetylgalactosaminyltransferase (GTA) and α-(1→3)-galactosyltransferase (GTB) catalyze the final step in ABO(H) blood group A and B antigen synthesis through sugar transfer from activated donor to the H antigen acceptor. These enzymes have a GT-A fold type with characteristic mobile polypeptide loops that cover the active site upon substrate binding and, despite intense investigation, many aspects of substrate specificity and catalysis remain unclear. The structures of GTA, GTB, and their chimeras have been determined to between 1.55 and 1.39 Å resolution in complex with natural donors UDP-Gal, UDP-Glc and, in an attempt to overcome one of the common problems associated with three-dimensional studies, the non-hydrolyzable donor analog UDP-phosphono-galactose (UDP-C-Gal). Whereas the uracil moieties of the donors are observed to maintain a constant location, the sugar moieties lie in four distinct conformations, varying from extended to the "tucked under" conformation associated with catalysis, each stabilized by different hydrogen bonding partners with the enzyme. Further, several structures show clear evidence that the donor sugar is disordered over two of the observed conformations and so provide evidence for stepwise insertion into the active site. Although the natural donors can both assume the tucked under conformation in complex with enzyme, UDP-C-Gal cannot. Whereas UDP-C-Gal was designed to be "isosteric" with natural donor, the small differences in structure imposed by changing the epimeric oxygen atom to carbon appear to render the enzyme incapable of binding the analog in the active conformation and so preclude its use as a substrate mimic in GTA and GTB.


    Organizational Affiliation

    From the Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 3P6, Canada and svevans@uvic.ca.,From the Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 3P6, Canada and.,the Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histo-blood group ABO system transferase
A
298Homo sapiensMutation(s): 2 
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
URM
Query on URM

Download SDF File 
Download CCD File 
A
(((2S,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl)methyl)phosphonic (((2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl)methyl phosphoric) anhydride
Uridine diphospho methylene galactopyranose
C16 H26 N2 O16 P2
WUPLBUVQIJIOHV-PPSAJGQHSA-N
 Ligand Interaction
MN
Query on MN

Download SDF File 
Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
DA8
Query on DA8

Download SDF File 
Download CCD File 
A
octyl 3-deoxy-2-O-(6-deoxy-alpha-L-galactopyranosyl)-beta-D-xylo-hexopyranoside
Alpha-L-Fucp-(1,2)-Beta-D-3-deoxy-Galp-O(CH2)7CH3
C20 H38 O9
FBVFDKBCZLMLQT-PPCMOIRNSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.183 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 52.530α = 90.00
b = 149.550β = 90.00
c = 79.180γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
CrystalCleardata reduction
d*TREKdata scaling
Cootmodel building
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health ResearchCanadaMOP-77655

Revision History 

  • Version 1.0: 2015-09-23
    Type: Initial release
  • Version 1.1: 2015-09-30
    Type: Database references
  • Version 1.2: 2015-11-18
    Type: Data collection, Database references
  • Version 1.3: 2018-03-07
    Type: Data collection, Derived calculations