2NVU

Structure of APPBP1-UBA3~NEDD8-NEDD8-MgATP-Ubc12(C111A), a trapped ubiquitin-like protein activation complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.241 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Basis for a ubiquitin-like protein thioester switch toggling E1-E2 affinity.

Huang, D.T.Hunt, H.W.Zhuang, M.Ohi, M.D.Holton, J.M.Schulman, B.A.

(2007) Nature 445: 394-398

  • DOI: 10.1038/nature05490
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Ubiquitin-like proteins (UBLs) are conjugated by dynamic E1-E2-E3 enzyme cascades. E1 enzymes activate UBLs by catalysing UBL carboxy-terminal adenylation, forming a covalent E1 throught UBL thioester intermediate, and generating a thioester-linked E ...

    Ubiquitin-like proteins (UBLs) are conjugated by dynamic E1-E2-E3 enzyme cascades. E1 enzymes activate UBLs by catalysing UBL carboxy-terminal adenylation, forming a covalent E1 throught UBL thioester intermediate, and generating a thioester-linked E2 throught UBL product, which must be released for subsequent reactions. Here we report the structural analysis of a trapped UBL activation complex for the human NEDD8 pathway, containing NEDD8's heterodimeric E1 (APPBP1-UBA3), two NEDD8s (one thioester-linked to E1, one noncovalently associated for adenylation), a catalytically inactive E2 (Ubc12), and MgATP. The results suggest that a thioester switch toggles E1-E2 affinities. Two E2 binding sites depend on NEDD8 being thioester-linked to E1. One is unmasked by a striking E1 conformational change. The other comes directly from the thioester-bound NEDD8. After NEDD8 transfer to E2, reversion to an alternate E1 conformation would facilitate release of the E2 throught NEDD8 thioester product. Thus, transferring the UBL's thioester linkage between successive conjugation enzymes can induce conformational changes and alter interaction networks to drive consecutive steps in UBL cascades.


    Organizational Affiliation

    Howard Hughes Medical Institute, St Jude Children's Research Hospital, Memphis, Tennessee 38105, USA.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NEDD8-activating enzyme E1 regulatory subunitA536Homo sapiensMutation(s): 0 
Gene Names: APPBP1NAE1HPP1
Find proteins for Q13564 (Homo sapiens)
Explore Q13564 
Go to UniProtKB:  Q13564
NIH Common Fund Data Resources
PHAROS  Q13564
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Maltose binding protein/NEDD8-activating enzyme E1 catalytic subunit chimeraB805Homo sapiensMutation(s): 0 
Gene Names: UBE1CUBA3
EC: 6.3.2 (PDB Primary Data), 6.2.1 (UniProt)
Find proteins for Q8TBC4 (Homo sapiens)
Explore Q8TBC4 
Go to UniProtKB:  Q8TBC4
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PHAROS  Q8TBC4
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
NEDD8-conjugating enzyme Ubc12C180Homo sapiensMutation(s): 1 
Gene Names: UBE2MUBC12
EC: 6.3.2 (PDB Primary Data), 2.3.2 (UniProt)
Find proteins for P61081 (Homo sapiens)
Explore P61081 
Go to UniProtKB:  P61081
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PHAROS  P61081
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  • Reference Sequence

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
NEDD8I, J81Homo sapiensMutation(s): 0 
Gene Names: NEDD8
Find proteins for Q15843 (Homo sapiens)
Explore Q15843 
Go to UniProtKB:  Q15843
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PHAROS  Q15843
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download CCD File 
B
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.241 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 156.494α = 90
b = 156.494β = 90
c = 190.485γ = 120
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-01-30
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance