4FRM

Crystal Structure of BBBB+UDP+Gal at pH 7.0 with MPD as the cryoprotectant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

pH-induced conformational changes in human ABO(H) blood group glycosyltransferases confirm the importance of electrostatic interactions in the formation of the semi-closed state.

Johal, A.R.Blackler, R.J.Alfaro, J.A.Schuman, B.Borisova, S.Evans, S.V.

(2014) Glycobiology 24: 237-246

  • DOI: 10.1093/glycob/cwt098
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The homologous human ABO(H) A and B blood group glycosyltransferases GTA and GTB have two mobile polypeptide loops surrounding their active sites that serve to allow substrate access and product egress and to recognize and sequester substrates for ca ...

    The homologous human ABO(H) A and B blood group glycosyltransferases GTA and GTB have two mobile polypeptide loops surrounding their active sites that serve to allow substrate access and product egress and to recognize and sequester substrates for catalysis. Previous studies have established that these enzymes can move from the "open" state to the "semi-closed" then "closed" states in response to addition of a substrate. The contribution of electrostatic interactions to these conformational changes has now been demonstrated by the determination at various pH of the structures of GTA, GTB and the chimeric enzyme ABBA. At near-neutral pH, GTA displays the closed state in which both mobile loops order around the active site, whereas ABBA and GTB display the open state. At low pH, the apparent protonation of the DXD motif in GTA leads to the expulsion of the donor analog to yield the open state, whereas at high pH, both ABBA and GTB form the semi-closed state in which the first mobile loop becomes an ordered α-helix. Step-wise deprotonation of GTB in increments of 0.5 between pH 6.5 and 10.0 shows that helix ordering is gradual, which indicates that the formation of the semi-closed state is dependent on electrostatic forces consistent with the binding of substrate. Spectropolarimetric studies of the corresponding stand-alone peptide in solution reveal no tendency toward helix formation from pH 7.0 to 10.0, which shows that pH-dependent stability is a product of the larger protein environment and underlines the importance of substrate in active site ordering.


    Organizational Affiliation

    Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada V8W 3P6.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histo-blood group ABO system transferase
A
293Homo sapiensMutation(s): 0 
Gene Names: ABO
Find proteins for P16442 (Homo sapiens)
Go to Gene View: ABO
Go to UniProtKB:  P16442
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GAL
Query on GAL

Download SDF File 
Download CCD File 
A
BETA-D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-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: 1.9 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.173 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 52.203α = 90.00
b = 150.598β = 90.00
c = 79.353γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
PHASERphasing
DENZOdata reduction
REFMACrefinement
MxDCdata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-12-25
    Type: Initial release
  • Version 1.1: 2014-02-26
    Type: Database references
  • Version 1.2: 2017-11-15
    Type: Refinement description