2BF8 | pdb_00002bf8

Crystal structure of SUMO modified ubiquitin conjugating enzyme E2- 25K


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.279 (Depositor) 
  • R-Value Work: 
    0.210 (Depositor), 0.213 (DCC) 
  • R-Value Observed: 
    0.213 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 2BF8

This is version 1.2 of the entry. See complete history

Literature

Sumo Imodification of the Ubiquitin Conjugating Enzyme E2-25K

Pichler, A.Knipscheer, P.Oberhofer, E.Van Dijk, W.J.Korner, R.Velgaard Olsen, J.Jentsch, S.Melchior, F.Sixma, T.K.

(2005) Nat Struct Mol Biol 12: 264

  • DOI: https://doi.org/10.1038/nsmb903
  • Primary Citation Related Structures: 
    2BEP, 2BF8

  • PubMed Abstract: 

    Post-translational modification with small ubiquitin-related modifier (SUMO) alters the function of many proteins, but the molecular mechanisms and consequences of this modification are still poorly defined. During a screen for novel SUMO1 targets, we identified the ubiquitin-conjugating enzyme E2-25K (Hip2). SUMO attachment severely impairs E2-25K ubiquitin thioester and unanchored ubiquitin chain formation in vitro. Crystal structures of E2-25K(1-155) and of the E2-25K(1-155)-SUMO conjugate (E2-25K(*)SUMO) indicate that SUMO attachment interferes with E1 interaction through its location on the N-terminal helix. The SUMO acceptor site in E2-25K, Lys14, does not conform to the consensus site found in most SUMO targets (PsiKXE), and functions only in the context of an alpha-helix. In contrast, adjacent SUMO consensus sites are modified only when in unstructured peptides. The demonstration that secondary structure elements are part of SUMO attachment signals could contribute to a better prediction of SUMO targets.


  • Organizational Affiliation
    • University of Göttingen, Department of Biochemistry I, Humboldt Allee 23, 37073 Göttingen, Germany.

Macromolecule Content 

  • Total Structure Weight: 26.82 kDa 
  • Atom Count: 1,947 
  • Modeled Residue Count: 231 
  • Deposited Residue Count: 236 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
UBIQUITIN-CONJUGATING ENZYME E2-25 KDA159Bos taurusMutation(s): 0 
EC: 6.3.2.19 (PDB Primary Data), 2.3.2.23 (UniProt)
UniProt
Find proteins for P61085 (Bos taurus)
Explore P61085 
Go to UniProtKB:  P61085
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61085
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
UBIQUITIN-LIKE PROTEIN SMT3C77Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P63165 (Homo sapiens)
Explore P63165 
Go to UniProtKB:  P63165
PHAROS:  P63165
GTEx:  ENSG00000116030 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP63165
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.279 (Depositor) 
  • R-Value Work:  0.210 (Depositor), 0.213 (DCC) 
  • R-Value Observed: 0.213 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.391α = 90
b = 58.391β = 90
c = 162.842γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-02-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2023-12-13
    Changes: Data collection, Database references, Other, Refinement description