4IRQ

Crystal structure of catalytic domain of human beta1,4galactosyltransferase 7 in closed conformation in complex with manganese and UDP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structures of beta-1,4-galactosyltransferase 7 enzyme reveal conformational changes and substrate binding.

Tsutsui, Y.Ramakrishnan, B.Qasba, P.K.

(2013) J.Biol.Chem. 288: 31963-31970

  • DOI: 10.1074/jbc.M113.509984
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The β-1,4-galactosyltransferase 7 (β4GalT7) enzyme is involved in proteoglycan synthesis. In the presence of a manganese ion, it transfers galactose from UDP-galactose to xylose on a proteoglycan acceptor substrate. We present here the crystal struct ...

    The β-1,4-galactosyltransferase 7 (β4GalT7) enzyme is involved in proteoglycan synthesis. In the presence of a manganese ion, it transfers galactose from UDP-galactose to xylose on a proteoglycan acceptor substrate. We present here the crystal structures of human β4GalT7 in open and closed conformations. A comparison of these crystal structures shows that, upon manganese and UDP or UDP-Gal binding, the enzyme undergoes conformational changes involving a small and a long loop. We also present the crystal structures of Drosophila wild-type β4GalT7 and D211N β4GalT7 mutant enzymes in the closed conformation in the presence of the acceptor substrate xylobiose and the donor substrate UDP-Gal, respectively. To understand the catalytic mechanism, we have crystallized the ternary complex of D211N β4GalT7 mutant enzyme in the presence of manganese with the donor and the acceptor substrates together in the same crystal structure. The galactose moiety of the bound UDP-Gal molecule forms seven hydrogen bonds with the protein molecule. The nonreducing end of the xylose moiety of xylobiose binds to the hydrophobic acceptor sugar binding pocket created by the conformational changes, whereas its extended xylose moiety forms hydrophobic interactions with a Tyr residue. In the ternary complex crystal structure, the nucleophile O4 oxygen atom of the xylose molecule is found in close proximity to the C1 and O5 atoms of the galactose moiety. This is the first time that a Michaelis complex of a glycosyltransferase has been described, and it clearly suggests an SN2 type catalytic mechanism for the β4GalT7 enzyme.


    Organizational Affiliation

    From the Structural Glycobiology Section and Basic Research Program, SAIC-Frederick, Inc., Nanobiology Program, Center for Cancer Research, NCI, National Institutes of Health, Frederick, Maryland 21702.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-1,4-galactosyltransferase 7
A, B, C, D
251Homo sapiensMutation(s): 0 
Gene Names: B4GALT7 (XGALT1)
EC: 2.4.1.-
Find proteins for Q9UBV7 (Homo sapiens)
Go to Gene View: B4GALT7
Go to UniProtKB:  Q9UBV7
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

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

Download SDF File 
Download CCD File 
A, B, C, D
URIDINE-5'-DIPHOSPHATE
C9 H14 N2 O12 P2
XCCTYIAWTASOJW-XVFCMESISA-N
 Ligand Interaction
TRS
Query on TRS

Download SDF File 
Download CCD File 
A, B, C, D
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.185 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 67.122α = 90.00
b = 121.532β = 95.12
c = 97.137γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data scaling
PHENIXrefinement
HKL-2000data reduction
PHENIXmodel building
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-09-25
    Type: Initial release
  • Version 1.1: 2015-02-25
    Type: Database references