4AP6

Crystal structure of human POFUT2 E54A mutant in complex with GDP- fucose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.195 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structure of Human Pofut2: Insights Into Thrombospondin Type 1 Repeat Fold and O-Fucosylation.

Chen, C.I.Keusch, J.J.Klein, D.Hess, D.Hofsteenge, J.Gut, H.

(2012) EMBO J 31: 3183

  • DOI: https://doi.org/10.1038/emboj.2012.143
  • Primary Citation of Related Structures:  
    4AP5, 4AP6

  • PubMed Abstract: 

    Protein O-fucosylation is a post-translational modification found on serine/threonine residues of thrombospondin type 1 repeats (TSR). The fucose transfer is catalysed by the protein O-fucosyltransferase 2 (POFUT2) and >40 human proteins contain the TSR consensus sequence for POFUT2-dependent fucosylation. To better understand O-fucosylation on TSR, we carried out a structural and functional analysis of human POFUT2 and its TSR substrate. Crystal structures of POFUT2 reveal a variation of the classical GT-B fold and identify sugar donor and TSR acceptor binding sites. Structural findings are correlated with steady-state kinetic measurements of wild-type and mutant POFUT2 and TSR and give insight into the catalytic mechanism and substrate specificity. By using an artificial mini-TSR substrate, we show that specificity is not primarily encoded in the TSR protein sequence but rather in the unusual 3D structure of a small part of the TSR. Our findings uncover that recognition of distinct conserved 3D fold motifs can be used as a mechanism to achieve substrate specificity by enzymes modifying completely folded proteins of very wide sequence diversity and biological function.


  • Organizational Affiliation

    Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GDP-FUCOSE PROTEIN O-FUCOSYLTRANSFERASE 2
A, B, C, D
422Homo sapiensMutation(s): 1 
EC: 2.4.1.221
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y2G5 (Homo sapiens)
Explore Q9Y2G5 
Go to UniProtKB:  Q9Y2G5
PHAROS:  Q9Y2G5
GTEx:  ENSG00000186866 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y2G5
Glycosylation
Glycosylation Sites: 3Go to GlyGen: Q9Y2G5-3
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GFB
Query on GFB

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
M [auth C],
Q [auth D]
GUANOSINE-5'-DIPHOSPHATE-BETA-L-FUCOPYRANOSE
C16 H25 N5 O15 P2
LQEBEXMHBLQMDB-JGQUBWHWSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
F [auth A]
I [auth B]
J [auth B]
K [auth B]
N [auth C]
F [auth A],
I [auth B],
J [auth B],
K [auth B],
N [auth C],
O [auth C]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
G [auth A],
L [auth B],
P [auth C],
R [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.195 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 153.01α = 90
b = 153.01β = 90
c = 185.68γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-08-08
    Type: Initial release
  • Version 1.1: 2012-09-26
    Changes: Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Other, Structure summary
  • Version 1.3: 2024-11-13
    Changes: Data collection, Database references, Structure summary