3F92 | pdb_00003f92

Crystal structure of ubiquitin-conjugating enzyme E2-25kDa (Huntington Interacting Protein 2) M172A mutant crystallized at pH 8.5

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 
    0.213 (Depositor), 0.217 (DCC) 
  • R-Value Work: 
    0.172 (Depositor), 0.178 (DCC) 
  • R-Value Observed: 
    0.174 (Depositor) 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history. 

Literature

Structure of full-length ubiquitin-conjugating enzyme E2-25K (huntingtin-interacting protein 2).

Wilson, R.C., Hughes, R.C., Flatt, J.W., Meehan, E.J., Ng, J.D., Twigg, P.D.

(2009) Acta Crystallogr Sect F Struct Biol Cryst Commun 65: 440-444

  • DOI: https://doi.org/10.1107/S1744309109011117
  • Primary Citation Related Structures: 
    3E46, 3F92

  • PubMed Abstract: 

    The ubiquitin-conjugating enzyme E2-25K has been identified as a huntingtin (the key protein in Huntington's disease) interacting protein and has been shown to play a role in mediating the toxicity of Abeta, the principal protein involved in Alzheimer's disease pathogenesis. E2-25K is a dual-domain protein with an ubiquitin-associated (UBA) domain as well as a conserved ubiquitin-conjugating (UBC) domain which catalyzes the formation of a covalent bond between the C-terminal glycine of an ubiquitin molecule and the -amine of a lysine residue on the acceptor protein as part of the ubiquitin-proteasome pathway. The crystal structures of E2-25K M172A mutant protein at pH 6.5 and pH 8.5 were determined to 1.9 and 2.2 A resolution, respectively. Examination of the structures revealed domain-domain interactions between the UBC and UBA domains which have not previously been reported.

    • Organizational Affiliation: 
    • University of Alabama in Huntsville, 35899, USA.

Macromolecule Content 

  • Total Structure Weight: 28.83 kDa 
  • Atom Count: 1,722 
  • Modeled Residue Count: 202 
  • Deposited Residue Count: 253 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Ubiquitin-conjugating enzyme E2 K253Homo sapiensMutation(s): 1 
Gene Names: UBE2K, HIP2, LIG
EC: 2.3.2.23
UniProt & NIH Common Fund Data Resources
Find proteins for P61086 (Homo sapiens)
Explore P61086 
Go to UniProtKB:  P61086
PHAROS:  P61086
GTEx:  ENSG00000078140 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61086
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free:  0.213 (Depositor), 0.217 (DCC) 
  • R-Value Work:  0.172 (Depositor), 0.178 (DCC) 
  • R-Value Observed: 0.174 (Depositor) 
Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 134.817α = 90
b = 134.817β = 90
c = 38.211γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-11-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-06-28
    Changes: Database references, Refinement description, Source and taxonomy, Structure summary
  • Version 1.3: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description