4AP6 | pdb_00004ap6

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 (Depositor), 0.234 (DCC) 
  • R-Value Work: 
    0.192 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.195 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4AP6

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 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.

Macromolecule Content 

  • Total Structure Weight: 202.04 kDa 
  • Atom Count: 13,222 
  • Modeled Residue Count: 1,555 
  • Deposited Residue Count: 1,688 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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: 2Go to GlyGen: Q9Y2G5-3
Sequence Annotations
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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 (Depositor), 0.234 (DCC) 
  • R-Value Work:  0.192 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.195 (Depositor) 
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

View Full Validation Report



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