4N39

Crystal structure of human O-GlcNAc transferase bound to a peptide from HCF-1 pro-repeat 2 (11-26)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 
    0.216 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.187 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.189 (Depositor) 

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Ligand Structure Quality Assessment 

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Literature

HCF-1 is cleaved in the active site of O-GlcNAc transferase.

Lazarus, M.B.Jiang, J.Kapuria, V.Bhuiyan, T.Janetzko, J.Zandberg, W.F.Vocadlo, D.J.Herr, W.Walker, S.

(2013) Science 342: 1235-1239

  • DOI: https://doi.org/10.1126/science.1243990
  • Primary Citation of Related Structures:  
    4N39, 4N3A, 4N3B, 4N3C

  • PubMed Abstract: 

    Host cell factor-1 (HCF-1), a transcriptional co-regulator of human cell-cycle progression, undergoes proteolytic maturation in which any of six repeated sequences is cleaved by the nutrient-responsive glycosyltransferase, O-linked N-acetylglucosamine (O-GlcNAc) transferase (OGT). We report that the tetratricopeptide-repeat domain of O-GlcNAc transferase binds the carboxyl-terminal portion of an HCF-1 proteolytic repeat such that the cleavage region lies in the glycosyltransferase active site above uridine diphosphate-GlcNAc. The conformation is similar to that of a glycosylation-competent peptide substrate. Cleavage occurs between cysteine and glutamate residues and results in a pyroglutamate product. Conversion of the cleavage site glutamate into serine converts an HCF-1 proteolytic repeat into a glycosylation substrate. Thus, protein glycosylation and HCF-1 cleavage occur in the same active site.


  • Organizational Affiliation

    Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit723Homo sapiensMutation(s): 0 
Gene Names: OGT
EC: 2.4.1.255
UniProt & NIH Common Fund Data Resources
Find proteins for O15294 (Homo sapiens)
Explore O15294 
Go to UniProtKB:  O15294
PHAROS:  O15294
GTEx:  ENSG00000147162 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO15294
Sequence Annotations
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Host cell factor 116Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P51610 (Homo sapiens)
Explore P51610 
Go to UniProtKB:  P51610
PHAROS:  P51610
GTEx:  ENSG00000172534 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP51610
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UDP
Query on UDP

Download Ideal Coordinates CCD File 
C [auth A]URIDINE-5'-DIPHOSPHATE
C9 H14 N2 O12 P2
XCCTYIAWTASOJW-XVFCMESISA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
UDP BindingDB:  4N39 IC50: 1800 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free:  0.216 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.187 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.189 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.17α = 90
b = 101.17β = 90
c = 131.73γ = 120
Software Package:
Software NamePurpose
SCALAdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
CBASSdata collection
iMOSFLMdata reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted UDPClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-01-01
    Type: Initial release
  • Version 1.1: 2024-02-28
    Changes: Data collection, Database references, Derived calculations