1TT5

Structure of APPBP1-UBA3-Ubc12N26: a unique E1-E2 interaction required for optimal conjugation of the ubiquitin-like protein NEDD8


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.237 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

A unique E1-E2 interaction required for optimal conjugation of the ubiquitin-like protein NEDD8.

Huang, D.T.Miller, D.W.Mathew, R.Cassell, R.Holton, J.M.Roussel, M.F.Schulman, B.A.

(2004) Nat Struct Mol Biol 11: 927-935

  • DOI: https://doi.org/10.1038/nsmb826
  • Primary Citation of Related Structures:  
    1TT5

  • PubMed Abstract: 

    Ubiquitin-like proteins (UBLs) such as NEDD8 are transferred to their targets by distinct, parallel, multienzyme cascades that involve the sequential action of E1, E2 and E3 enzymes. How do enzymes within a particular UBL conjugation cascade interact with each other? We report here that the unique N-terminal sequence of NEDD8's E2, Ubc12, selectively recruits NEDD8's E1 to promote thioester formation between Ubc12 and NEDD8. A peptide corresponding to Ubc12's N terminus (Ubc12N26) specifically binds and inhibits NEDD8's E1, the heterodimeric APPBP1-UBA3 complex. The structure of APPBP1-UBA3- Ubc12N26 reveals conserved Ubc12 residues docking in a groove generated by loops conserved in UBA3s but not other E1s. These data explain why the Ubc12-UBA3 interaction is unique to the NEDD8 pathway. These studies define a novel mechanism for E1-E2 interaction and show how enzymes within a particular UBL conjugation cascade can be tethered together by unique protein-protein interactions emanating from their common structural scaffolds.


  • Organizational Affiliation

    Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
amyloid protein-binding protein 1
A, C
531Homo sapiensMutation(s): 0 
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Find proteins for Q13564 (Homo sapiens)
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Go to UniProtKB:  Q13564
PHAROS:  Q13564
GTEx:  ENSG00000159593 
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UniProt GroupQ13564
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ubiquitin-activating enzyme E1C isoform 1
B, D
434Homo sapiensMutation(s): 0 
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Find proteins for Q8TBC4 (Homo sapiens)
Explore Q8TBC4 
Go to UniProtKB:  Q8TBC4
PHAROS:  Q8TBC4
GTEx:  ENSG00000144744 
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UniProt GroupQ8TBC4
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-conjugating enzyme E2 M
E, F
26Homo sapiensMutation(s): 0 
Gene Names: UBE2MUBC12
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Find proteins for P61081 (Homo sapiens)
Explore P61081 
Go to UniProtKB:  P61081
PHAROS:  P61081
GTEx:  ENSG00000130725 
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UniProt GroupP61081
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.237 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.41α = 90
b = 122.77β = 90
c = 195.91γ = 90
Software Package:
Software NamePurpose
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-09-14
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Derived calculations