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

    Department of Integrative Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS, INSERM, UdS, 1 rue Laurent Fries, 67404, Illkirch CEDEX, France.,Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, E-08193 Cerdanyola del Vallès, Spain. Electronic address: Guillem.Prats.Ejarque@uab.cat.,PRESTO, JST, Nagoya 464-8601, Japan.,Department of Chemistry, University of York, Heslington, York, YO10 5DD, United Kingdom.,RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.,Center for Electron Microscopy Research, Korea Basic Science Institute, Ochang, Chungbuk, 28119, Republic of Korea.,School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK. j.angulo@uea.ac.uk.,Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, E-08193 Cerdanyola del Vallès, Spain. Electronic address: Mohammed.Moussaoui@uab.cat.,Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India.,Severance Biomedical Science Institute and Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea. jsshin6203@yuhs.ac.,Laboratoire d'Innovation Moléculaire et Applications, Université de Strasbourg|, Université de Haute-Alsace|, CNRS|, LIMA (UMR 7042), Equipe de Synthèse Organique et Molécules Bioactives (SYBIO), ECPM, 25 rue Becquerel, 67000, Strasbourg, France.,School of Cellular & Molecular Medicine , University of Bristol , Bristol BS8 1TD , U.K.,Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea. hscho8@yonsei.ac.kr.,Cell Adhesion Laboratory, Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, United States.,Division of Agronomy and Horticultural Science, Graduate School of Agriculture, Kyoto University, Uji-shi, Japan.,School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.,Center for Inflammation Research, University of Texas Southwestern Medical Center, Dallas, TX, USA. Zhijian.Chen@UTSouthwestern.edu.,Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA.,Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China.,Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China. shi-lab@tsinghua.edu.cn.,National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, CAS Center for Excellence on Molecular Cell Science, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 200031, Shanghai, China.,Department of Chemistry and Biology "A. Zambelli", University of Salerno, Via Giovanni Paolo II, 132, 84084, Fisciano, Salerno, Italy.,National Key Laboratory of Crop Genetic Improvement, Huazhong Agriculture University, 430072, Wuhan, China.,Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea.,Cambridge Institute for Medical Research and Department of Haematology, University of Cambridge, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 0XY, England.,Department of Biophysics, All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110 029, India tpsingh.aiims@gmail.com.,Department of Bioengineering, Stanford University, Stanford, CA, USA.,Department of Biology , University of Waterloo , Waterloo , Ontario , Canada N2L 3G1.,Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China.,Department of Chemistry, College of Science , University of Hail , Saudi Arabia.,Shanghai Institute of Precision Medicine, 200125, Shanghai, China. huangchh@shsmu.edu.cn.,Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.,Key laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, China. leim@shsmu.edu.cn.,Department of Physiology and Systems Bioscience, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan.,Institute of Transformative Bio-Molecules, Nagoya University, Nagoya 464-8601, Japan.,The Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, 66045.,Section of Structural Biology, Department of Medicine, Imperial College London, London SW7 2AZ, UK. Electronic address: d.wigley@imperial.ac.uk.,Department of Biochemistry, University of Washington, Seattle, WA, USA.,Instituto de Física de Líquidos y Sistemas Biológicos, CONICET, UNLP, Calle 59 No. 789, La Plata, Argentina.,Department of Chemistry and Biochemistry , Laurentian University , Sudbury , Ontario , Canada P3E 2C6.,School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, 61005, Republic of Korea.,Department of Stem Cell Biology and Medicine/Cancer Stem Cell Research, Kyushu University Graduate School of Medical Sciences, Fukuoka 812-8582, Japan.,Crown Bioscience, Taicang, China.,Applied Biotechnology Group, Biomedical Science School, Universidad Europea de Madrid, Urbanización El Bosque, Calle Tajo, s/n, 28670, Villaviciosa de Odón, Spain; Grupo de Investigación en Desarrollo Agroindustrial Sostenible, Universidad de la Costa, CUC, Calle 58 # 55 - 66, Barranquilla, Colombia. Electronic address: jesus.fernandez2@universidadeuropea.es.,MRC Laboratory of Molecular Biology, Cambridge, UK.,Department of Chemistry, University of Washington, Seattle, WA, USA.,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.,Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya 464-8601, Japan.,Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA. dabaker@uw.edu.,Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, Wood Lane, London W12 0BZ, England.,Department of Applied Chemistry, Waseda University, Tokyo 169-8555, Japan.,Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA. Xuewu.Zhang@UTSouthwestern.edu.,Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.,MRC Laboratory of Molecular Biology, Cambridge, UK. scheres@mrc-lmb.cam.ac.uk.,Division of Basic Science, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,ERATO Itami Molecular Nanocarbon Project, JST, Nagoya 464-8601, Japan.,College of Veterinary Medicine, Kansas State University, Manhattan, KS, 66506, USA.,Molecular Biophysics and Integrated Bioimaging, Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Department of Biophysics, All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110 029, India.,The Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama, 36849.,Molecular Biophysics and Integrated Bioimaging, Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, California, USA.,Department of Health Sciences, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan.,Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Department of Physics, Graduate School of Science, Nagoya University, Nagoya 464-8601, Japan, and RIKEN Center for Computational Science, Kobe 650-0047, Japan.,Vollum Institute, Oregon Health & Science University, Portland, United States.,Department of Microbiology, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea.,Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, E-08193 Cerdanyola del Vallès, Spain.,Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China. shi-lab@tsinghua.edu.cn.,Division for Structural Biochemistry, OE8830, Hannover Medical School, Hannover, Germany.,Laboratory of Molecular Physiology, NHLBI, National Institutes of Health, Bethesda, United States.,Graduate School of Science, Osaka Prefecture University, Osaka 599-8531, Japan.,Center for Drug Discovery, Northeastern University, Boston, MA 02115, USA.,School of Pharmacy , University of Waterloo , Waterloo , Ontario , Canada N2L 3G1.,Institute of Biotechnology, Vilnius University, Vilnius, Lithuania. Electronic address: siksnys@ibt.lt.,Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA 02115, USA. Electronic address: c.mattos@northeastern.edu.,Fundación ARAID, 50018, Zaragoza, Spain. rhurtado@bifi.es.,Centre for Structural Systems Biology (CSSB), German Electron Synchrotron (DESY), Hamburg, Germany.,Department of Biochemistry, University of Washington, Seattle, WA, USA. dabaker@uw.edu.,Section of Structural Biology, Department of Medicine, Imperial College London, London SW7 2AZ, UK.,Institute for Protein Design, University of Washington, Seattle, WA, USA.,Department of Microbiology, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea. jsshin6203@yuhs.ac.,Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA. Zhijian.Chen@UTSouthwestern.edu.,Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA. Zhijian.Chen@UTSouthwestern.edu.,Faculty of Natural Sciences, Department of Life Sciences, Imperial College London, Exhibition Road, South Kensington, London SW7 2AZ, England.,Institute for Biophysical Chemistry, OE4350, Hannover Medical School, Hannover, Germany.,Institute for Protein Design, University of Washington, Seattle, WA, USA. dabaker@uw.edu.,Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA. Xiaochen.Bai@UTSouthwestern.edu.,Institute of Biotechnology, Vilnius University, Vilnius, Lithuania.,Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, E-08193 Cerdanyola del Vallès, Spain. Electronic address: Ester.Boix@uab.cat.,Department of Physiology, Faculty of Medicine, Saitama Medical University, Saitama 350-0495, Japan.,Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA 02115, USA.,John Harvard Distinguished Science Fellowship Program, Harvard University, Cambridge, MA, USA.,Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA. Xiaochen.Bai@UTSouthwestern.edu.,Department of Chemistry , University of Waterloo , Waterloo , Ontario , Canada N2L 3G1.,MRC Laboratory of Molecular Biology, Cambridge, UK. mg@mrc-lmb.cam.ac.uk.,Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 200011, Shanghai, China. huangchh@shsmu.edu.cn.,Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA. Xuewu.Zhang@UTSouthwestern.edu.,Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, E-08193 Cerdanyola del Vallès, Spain. Electronic address: Victoria.Nogues@uab.cat.,Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 200011, Shanghai, China.,Department of Physiology and Advanced Research Center for Medical Science, Toho University School of Medicine, Tokyo 143-8540, Japan.,Center for Advanced Medical Innovation, Kyushu University, Fukuoka 812-8582, Japan.,Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA.,Shanghai Institute of Precision Medicine, 200125, Shanghai, China.,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 Applied Chemistry and Biotechnology, Graduate School of Engineering, University of Fukui, Fukui-shi, Japan.,Technology Center for Protein Sciences, Ministry of Education Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing, China.,Shanghai Institute of Precision Medicine, 200125, Shanghai, China. leim@shsmu.edu.cn.,BIFI, University of Zaragoza, BIFI-IQFR (CSIC) Joint Unit, Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, Zaragoza, 50018, Spain.,BIFI, University of Zaragoza, BIFI-IQFR (CSIC) Joint Unit, Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, Zaragoza, 50018, Spain. rhurtado@bifi.es.,Department of Technical Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, Stuttgart, Germany.,Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 200011, Shanghai, China. leim@shsmu.edu.cn.,Applied Biotechnology Group, Biomedical Science School, Universidad Europea de Madrid, Urbanización El Bosque, Calle Tajo, s/n, 28670, Villaviciosa de Odón, Spain.




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