3ZY5

Crystal structure of POFUT1 in complex with GDP-fucose (crystal-form-I)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.219 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structural Insights Into the Mechanism of Protein O-Fucosylation.

Lira-Navarrete, E.Valero-Gonzalez, J.Villanueva, R.Martinez-Julvez, M.Tejero, T.Merino, P.Panjikar, S.Hurtado-Guerrero, R.

(2011) PLoS One 6: 25365

  • DOI: 10.1371/journal.pone.0025365
  • Primary Citation of Related Structures:  
    3ZY2, 3ZY3, 3ZY4, 3ZY5, 3ZY6

  • PubMed Abstract: 
  • Protein O-fucosylation is an essential post-translational modification, involved in the folding of target proteins and in the role of these target proteins during embryonic development and adult tissue homeostasis, among other things. Two different enzymes are responsible for this modification, Protein O-fucosyltransferase 1 and 2 (POFUT1 and POFUT2, respectively) ...

    Protein O-fucosylation is an essential post-translational modification, involved in the folding of target proteins and in the role of these target proteins during embryonic development and adult tissue homeostasis, among other things. Two different enzymes are responsible for this modification, Protein O-fucosyltransferase 1 and 2 (POFUT1 and POFUT2, respectively). Both proteins have been characterised biologically and enzymatically but nothing is known at the molecular or structural level. Here we describe the first crystal structure of a catalytically functional POFUT1 in an apo-form and in complex with GDP-fucose and GDP. The enzyme belongs to the GT-B family and is not dependent on manganese for activity. GDP-fucose/GDP is localised in a conserved cavity connected to a large solvent exposed pocket, which we show is the binding site of epidermal growth factor (EGF) repeats in the extracellular domain of the Notch Receptor. Through both mutational and kinetic studies we have identified which residues are involved in binding and catalysis and have determined that the Arg240 residue is a key catalytic residue. We also propose a novel S(N)1-like catalytic mechanism with formation of an intimate ion pair, in which the glycosidic bond is cleaved before the nucleophilic attack; and theoretical calculations at a DFT (B3LYP/6-31+G(d,p) support this mechanism. Thus, the crystal structure together with our mutagenesis studies explain the molecular mechanism of POFUT1 and provide a new starting point for the design of functional inhibitors to this critical enzyme in the future.


    Organizational Affiliation

    Institute of Biocomputation and Physics of Complex Systems, University of Zaragoza, Zaragoza, Spain.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PUTATIVE GDP-FUCOSE PROTEIN O-FUCOSYLTRANSFERASE 1A362Caenorhabditis elegansMutation(s): 0 
Gene Names: C15C7.7
EC: 2.4.1.221
UniProt
Find proteins for Q18014 (Caenorhabditis elegans)
Explore Q18014 
Go to UniProtKB:  Q18014
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ18014
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GFB
Query on GFB

Download Ideal Coordinates CCD File 
F [auth A]GUANOSINE-5'-DIPHOSPHATE-BETA-L-FUCOPYRANOSE
C16 H25 N5 O15 P2
LQEBEXMHBLQMDB-JGQUBWHWSA-N
 Ligand Interaction
BTB
Query on BTB

Download Ideal Coordinates CCD File 
G [auth A]2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C8 H19 N O5
OWMVSZAMULFTJU-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A],
E [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
GFB Binding MOAD:  3ZY5 Kd: 230 (nM) from 1 assay(s)
PDBBind:  3ZY5 Kd: 230 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.219 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.543α = 90
b = 42.53β = 107.63
c = 97.663γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2011-09-14
    Type: Initial release
  • Version 1.1: 2011-10-12
    Changes: Database references
  • Version 1.2: 2018-04-04
    Changes: Data collection