Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 26.82 kDa 
• Atom Count: 1947 
• Residue Count: 231 
• Unique protein chains: 2

2BF8

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

• DOI: 10.2210/pdb2BF8/pdb

• Classification: LIGASE
• Organism(s): Bos taurus, Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2004-12-06 Released: 2005-02-16 
• Deposition Author(s): Pichler, A., Knipscheer, P., Oberhofer, E., Van Dijk, W.J., Korner, R., Velgaard Olsen, J., Jentsch, S., Melchior, F., Sixma, T.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.279 
• R-Value Work: 0.210 
• R-Value Observed: 0.213 

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

• PubMed: 15723079 
• DOI: 10.1038/nsmb903
• Structures With Same Primary Citation


• 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
UBIQUITIN-CONJUGATING ENZYME E2-25 KDA	A	159	Bos taurus	Mutation(s): 0  Gene Names: UBE2K, HIP2 EC: 6.3.2.19 (PDB Primary Data), 2.3.2.23 (UniProt)
Find proteins for P61085 (Bos taurus) Explore P61085  Go to UniProtKB:  P61085

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
UBIQUITIN-LIKE PROTEIN SMT3C	B	77	Homo sapiens	Mutation(s): 0  Gene Names: SUMO1, SMT3C, SMT3H3, UBL1, OK/SW-cl.43
Find proteins for P63165 (Homo sapiens) Explore P63165  Go to UniProtKB:  P63165
NIH Common Fund Data Resources
PHAROS  P63165 GTEx  ENSG00000116030

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.279 
• R-Value Work: 0.210 
• R-Value Observed: 0.213 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.391	α = 90
b = 58.391	β = 90
c = 162.842	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-12-06 
• Released Date: 2005-02-16 
Deposition Author(s): Pichler, A., Knipscheer, P., Oberhofer, E., Van Dijk, W.J., Korner, R., Velgaard Olsen, J., Jentsch, S., Melchior, F., Sixma, T.K.

Revision History 

• Version 1.0: 2005-02-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance