5CQL

GTB mutant with mercury - E303A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Glycosyltransfer in mutants of putative catalytic residue Glu303 of the human ABO(H) A and B blood group glycosyltransferases GTA and GTB proceeds through a labile active site.

Blackler, R.J.Gagnon, S.M.Polakowski, R.Rose, N.L.Zheng, R.B.Letts, J.A.Johal, A.R.Schuman, B.Borisova, S.N.Palcic, M.M.Evans, S.V.

(2017) Glycobiology 27: 370-380

  • DOI: 10.1093/glycob/cww117
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The homologous glycosyltransferases α-1,3-N-acetylgalactosaminyltransferase (GTA) and α-1,3-galactosyltransferase (GTB) carry out the final synthetic step of the closely related human ABO(H) blood group A and B antigens. The catalytic mechanism of th ...

    The homologous glycosyltransferases α-1,3-N-acetylgalactosaminyltransferase (GTA) and α-1,3-galactosyltransferase (GTB) carry out the final synthetic step of the closely related human ABO(H) blood group A and B antigens. The catalytic mechanism of these model retaining enzymes remains under debate, where Glu303 has been suggested to act as a putative nucleophile in a double displacement mechanism, a local dipole stabilizing the intermediate in an orthogonal associative mechanism or a general base to stabilize the reactive oxocarbenium ion-like intermediate in an SNi-like mechanism. Kinetic analysis of GTA and GTB point mutants E303C, E303D, E303Q and E303A shows that despite the enzymes having nearly identical sequences, the corresponding mutants of GTA/GTB have up to a 13-fold difference in their residual activities relative to wild type. High-resolution single crystal X-ray diffraction studies reveal, surprisingly, that the mutated Cys, Asp and Gln functional groups are no more than 0.8 Å further from the anomeric carbon of donor substrate compared to wild type. However, complicating the analysis is the observation that Glu303 itself plays a critical role in maintaining the stability of a strained "double-turn" in the active site through several hydrogen bonds, and any mutation other than E303Q leads to significantly higher thermal motion or even disorder in the substrate recognition pockets. Thus, there is a remarkable juxtaposition of the mutants E303C and E303D, which retain significant activity despite disrupted active site architecture, with GTB/E303Q, which maintains active site architecture but exhibits zero activity. These findings indicate that nucleophilicity at position 303 is more catalytically valuable than active site stability and highlight the mechanistic elasticity of these enzymes.


    Organizational Affiliation

    Department of Biochemistry and Microbiology, University of Victoria, PO Box 3800, STN CSC, Victoria, BC, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histo-blood group ABO system transferase
X
294Homo sapiensMutation(s): 1 
Gene Names: ABO
Find proteins for P16442 (Homo sapiens)
Go to Gene View: ABO
Go to UniProtKB:  P16442
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HG
Query on HG

Download SDF File 
Download CCD File 
X
MERCURY (II) ION
Hg
BQPIGGFYSBELGY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.174 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 52.490α = 90.00
b = 150.210β = 90.00
c = 79.230γ = 90.00
Software Package:
Software NamePurpose
CrystalCleardata reduction
MOLREPphasing
PDB_EXTRACTdata extraction
d*TREKdata scaling
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-10-26
    Type: Initial release
  • Version 1.1: 2016-12-07
    Type: Database references
  • Version 1.2: 2017-01-11
    Type: Database references
  • Version 1.3: 2017-04-19
    Type: Database references
  • Version 1.4: 2018-03-07
    Type: Data collection