6IF1

Crystal structure of Ube2K and K48-linked di-ubiquitin complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.466 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Crystal structure of the Ube2K/E2-25K and K48-linked di-ubiquitin complex provides structural insight into the mechanism of K48-specific ubiquitin chain synthesis.

Lee, J.G.Youn, H.S.Kang, J.Y.Park, S.Y.Kidera, A.Yoo, Y.J.Eom, S.H.

(2018) Biochem. Biophys. Res. Commun. 506: 102-107

  • DOI: 10.1016/j.bbrc.2018.10.067

  • PubMed Abstract: 
  • Ubiquitin-conjugating enzymes (E2) form thioester bonds with ubiquitin (Ub), which are subsequently transferred to target proteins for cellular progress. Ube2K/E2-25K (a class II E2 enzyme) contains a C-terminal ubiquitin-associated (UBA) domain that ...

    Ubiquitin-conjugating enzymes (E2) form thioester bonds with ubiquitin (Ub), which are subsequently transferred to target proteins for cellular progress. Ube2K/E2-25K (a class II E2 enzyme) contains a C-terminal ubiquitin-associated (UBA) domain that has been suggested to control ubiquitin recognition, dimerization, or poly-ubiquitin chain formation. Ube2K is a special E2 because it synthesizes K48-linked poly-ubiquitin chains without E3 ubiquitin ligase. We found that a novel interaction between the acceptor di-Ub (Ub 2 ) and the auxiliary Ube2K promotes the discharging reaction and production of tri-Ub (Ub 3 ), probably by guiding and positioning the K48 (in the distal Ub) of the acceptor Ub 2 in the active site. We also determined the crystal structure of Ube2K-Ub 2 at 2.47 Å resolution. Based on our structural and biochemical data, we proposed a structural model of Ub 3 synthesis by Ube2K without E3.


    Organizational Affiliation

    School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, 61005, Republic of Korea; Steitz Center for Structural Biology, Gwangju Institute of Science and Technology, Gwangju, 61005, Republic of Korea.,School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, 61005, Republic of Korea; Steitz Center for Structural Biology, Gwangju Institute of Science and Technology, Gwangju, 61005, Republic of Korea; Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju, 61005, Republic of Korea. Electronic address: eom@gist.ac.kr.,School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, 61005, Republic of Korea.,Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-conjugating enzyme E2 K
A, B
199Homo sapiensMutation(s): 0 
Gene Names: UBE2K (HIP2, LIG)
EC: 2.3.2.23
Find proteins for P61086 (Homo sapiens)
Go to Gene View: UBE2K
Go to UniProtKB:  P61086
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin
C, D
76Homo sapiensMutation(s): 0 
Gene Names: UBB
Find proteins for P0CG47 (Homo sapiens)
Go to Gene View: UBB
Go to UniProtKB:  P0CG47
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.466 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.215 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 41.559α = 90.00
b = 38.792β = 90.10
c = 190.321γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHASERphasing
PHENIXrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-11-21
    Type: Initial release