6DC6

Crystal structure of human ubiquitin activating enzyme E1 (Uba1) in complex with ubiquitin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.14 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of a human ubiquitin E1-ubiquitin complex reveals conserved functional elements essential for activity.

Lv, Z.Williams, K.M.Yuan, L.Atkison, J.H.Olsen, S.K.

(2018) J. Biol. Chem. 293: 18337-18352

  • DOI: 10.1074/jbc.RA118.003975

  • PubMed Abstract: 
  • Ubiquitin (Ub) signaling plays a key regulatory role in nearly every aspect of eukaryotic biology and is initiated by E1 enzymes that activate and transfer Ub to E2 Ub-conjugating enzymes. Despite Ub E1's fundamental importance to the cell and its at ...

    Ubiquitin (Ub) signaling plays a key regulatory role in nearly every aspect of eukaryotic biology and is initiated by E1 enzymes that activate and transfer Ub to E2 Ub-conjugating enzymes. Despite Ub E1's fundamental importance to the cell and its attractiveness as a target for therapeutic intervention in cancer and other diseases, its only available structural information is derived from yeast orthologs of human ubiquitin-like modifier-activating enzyme 1 (hUBA1). To illuminate structural differences between yeast and hUBA1 structures that might be exploited for the development of small-molecule therapeutics, we determined the first crystal structure of a hUBA1-Ub complex. Using structural analysis, molecular modeling, and biochemical analysis, we demonstrate that hUBA1 shares a conserved overall structure and mechanism with previously characterized yeast orthologs, but displays subtle structural differences, particularly within the active site. Computational analysis revealed four potential ligand-binding hot spots on the surface of hUBA1 that might serve as targets to inhibit hUBA1 at the level of Ub activation or E2 recruitment or that might potentially be used in approaches such as protein-targeting chimeric molecules. Taken together, our work enhances our understanding of the hUBA1 mechanism, provides an improved framework for the development of small-molecule inhibitors of UBA1, and serves as a stepping stone for structural studies that involve the enzymes of the human Ub system at the level of both E1 and E2.


    Organizational Affiliation

    Sprint Bioscience , 141 57 Huddinge , Sweden.,Infectious Diseases Discovery , GlaxoSmithKline , 1250 South Collegeville Road , Collegeville , Pennsylvania 19426 , United States.,College of Life Sciences, State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, People's Republic of China. Electronic address: zhouwh@nankai.edu.cn.,Antibody and Vaccine Group, Cancer Sciences Unit, University of Southampton Faculty of Medicine, Southampton SO16 6YD, UK; Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK.,Department of Chemistry and Technologies of Drugs, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy.,Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305.,Cleveland Center for Membrane and Structural Biology, Case Western Reserve University, Cleveland, OH 44106, USA.,Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba, Japan.,From the Department of Biochemistry and Molecular Biology and Hollings Cancer Center, Medical University of South Carolina, Charleston, South Carolina 29425 olsensk@musc.edu.,Institut de Biologie Structurale, Université Grenoble Alpes-CEA-CNRS, Grenoble, France.,Graduate School of Horticulture, Chiba University, Matsudo, Chiba, Japan.,Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Singapore.,Pohang Accelerator Laboratory, Pohang, Gyeongbuk, Republic of Korea.,Protein Core Facility, University of Southampton Faculty of Medicine, Southampton SO16 6YD, UK.,European Synchrotron Radiation Facility, 38043 Grenoble, France.,Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom. Electronic address: stuart.conway@chem.ox.ac.uk.,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305; kcgarcia@stanford.edu.,Scripps Research, United States.,School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom.,Charnwood Molecular , Loughborough LE11 5DA , U.K.,Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom.,Neuroscience, IMED Biotech Unit , AstraZeneca , Cambridge CB21 6GH , U.K.,Department of Hematology and Oncology, Center for Cancer Immune Therapy, Herlev Hospital, University of Copenhagen, Herlev, Denmark.,Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, U.K.,Beijing Advanced Innovation Center for Food Nutrition and Human Health, State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, 100193, China. chenzhongzhou@cau.edu.cn.,Asubio Pharma Co., Ltd., 6-4-3 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.,Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, Japan.,Higuchi Biosciences Center, University of Kansas, Lawrence, Kansas, 66047.,Henry Wellcome Building for Molecular Physiology, University of Oxford, Oxford, OX3 7BN, UK.,The Gut Health and Food Safety Programme, Quadram Bioscience Institute, NR4 7UA Norwich, United Kingdom.,Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, Japan. ts@chembio.t.u-tokyo.ac.jp.,Epigenetic Regulation of Chromatin Function Group, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K.,Program in Immunology, Stanford University School of Medicine, Stanford, CA 94305.,Department Molecular Oncology and Immunology, B6 Plesmanlaan 121, Amsterdam, 1066CX, The Netherlands.,Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA.,Pohang Accelerator Laboratory, Pohang, Gyeongbuk, Republic of Korea. jaehyun.park@postech.ac.kr.,Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale G. Fanin 40, I-40127 Bologna, Italy. stefano.ciurli@unibo.it.,Polgenix Inc., Cleveland, OH 44106, USA.,The Gut Health and Food Safety Programme, Quadram Bioscience Institute, NR4 7UA Norwich, United Kingdom; c.dong@uea.ac.uk nathalie.juge@quadram.ac.uk.,Departments of Biophysics, UT Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, Texas, 75390.,BioMedical Research Centre, University of East Anglia, NR4 7TJ Norwich, United Kingdom; c.dong@uea.ac.uk nathalie.juge@quadram.ac.uk.,Moscow Institute of Physics and Technology, Dolgoprudniy, Russia.,Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK; Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK.,Department of Chemistry , Vanderbilt University , Nashville , Tennessee 37232-0146 , United States.,College of Life Sciences, College of Pharmacy, State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, People's Republic of China.,Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, 112, Taiwan.,Nuffield Department of Medicine Research Building, Roosevelt Drive, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK.,BioMedical Research Centre, University of East Anglia, NR4 7TJ Norwich, United Kingdom.,Department of Biochemistry, National University of Singapore, Singapore.,Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Japan.,Immunocore LTD, Oxford, United Kingdom.,School of Pharmacy, University of East Anglia, NR4 7TJ Norwich, United Kingdom.,Antibody and Vaccine Group, Cancer Sciences Unit, University of Southampton Faculty of Medicine, Southampton SO16 6YD, UK.,Antibody and Vaccine Group, Cancer Sciences Unit, University of Southampton Faculty of Medicine, Southampton SO16 6YD, UK. Electronic address: ann.white@ucb.com.,Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, Japan tendo@cc.kyoto-su.ac.jp.,Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305.,Max Planck Institute of Biophysics, Frankfurt am Main, Germany.,Japan Science and Technology Agency/Core Research for Evolutional Science and Technology, Nagoya University, Nagoya, Japan.,College of Life Sciences, State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, People's Republic of China.,Cardiovascular and Metabolic Diseases, IMED Biotech Unit , AstraZeneca , 141 57 Huddinge , Sweden.,Department of Medicinal Chemistry, Faculty of Pharmaceutical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark.,Henry Wellcome Building for Molecular Physiology, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7LD, U.K.,Department of Molecular Biology and Biochemistry , Simon Fraser University , Burnaby , British Columbia V5A 1S6 , Canada.,Boehringer Ingelheim RCV GmbH & Co. KG , Doktor-Boehringer-Gasse 5-11 , 1120 Vienna , Austria.,Division of Structural Biology, Wellcome Centre for Human Genetics, Roosevelt Drive, University of Oxford, Oxford, OX3 7BN, UK.,Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya, Japan.,CRUK/MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, United Kingdom.,Department of Chemistry , Simon Fraser University , Burnaby , British Columbia V5A 1S6 , Canada . Email: dvocadlo@sfu.ca.,Institute of Biochemistry, ETH Zürich, Zürich, Switzerland.,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305.,Institute for Protein Dynamics, Kyoto Sangyo University, Kyoto, Japan.,School of Life Sciences, Anhui University, 111 Jiulong Road, Hefei, Anhui, 230601, China; Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, 111 Jiulong Road, Hefei, Anhui, 230601, China.,School of Chemistry and Biochemistry , The University of Western Australia (M313) , 35 Stirling Highway , Crawley , WA 6009 , Australia.,Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India.,Department of Food Science, National (Taiwan) Ocean University, Keelung, 202, Taiwan.,Protein Structure Laboratory, Del Shankel Structural Biology Center, University of Kansas, Lawrence, KS, 66045.,From the Department of Biochemistry and Molecular Biology and Hollings Cancer Center, Medical University of South Carolina, Charleston, South Carolina 29425.,Hamburg Centre for Ultrafast Imaging & Institute for Nanostructure and Solid State Physics, University of Hamburg, 20146 Hamburg, Germany.,Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 3TA, United Kingdom.,Department of Biology, Faculty of Science, Niigata University, Ikarashi 2-8050, Nishi-ku, Niigata 950-2181, Japan.,Beijing Advanced Innovation Center for Food Nutrition and Human Health, State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, 100193, China.,School of Life Sciences, Anhui University, 111 Jiulong Road, Hefei, Anhui, 230601, China. Electronic address: tangrp99@iccas.ac.cn.,NTU Institute of Structural Biology, Nanyang Technological University, 59 Nanyang Drive, 636921, Singapore.,Division of Cardiovascular Medicine, Radcliffe Department of Medicine, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7LD, UK.,Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, Japan.,Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing, 100048, China.,Discovery Sciences, IMED Biotech Unit , AstraZeneca , S-43183 Mölndal , Sweden.,Japan Science and Technology Agency/Core Research for Evolutional Science and Technology, Kyoto Sangyo University, Kyoto, Japan.,Discovery Safety, Drug Safety and Metabolism, IMED Biotech Unit , AstraZeneca , Waltham , Massachusetts 02451 , United States.,Medicines Discovery Institute , Cardiff University , Main Building, Park Place , Cardiff CF10 3AT , United Kingdom.,Division of Biotechnology, Korea University, Seoul, Republic of Korea. structures@korea.ac.kr.,Laboratório de Cristalografia de Proteínas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil.,School of Life Sciences, Anhui University, 111 Jiulong Road, Hefei, Anhui, 230601, China; Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, 111 Jiulong Road, Hefei, Anhui, 230601, China. Electronic address: zhmin07@ahu.edu.cn.,Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, 117543, Singapore.,College of Life Sciences, Tianjin University, Tianjin, 300071, People's Republic of China.,Systems Immunity Research Institute, Cardiff University School of Medicine, Cardiff, United Kingdom.,Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, M5S 1A8, Canada.,Asubio Pharma Co., Ltd., 6-4-3 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan. Electronic address: muto.tsuyoshi.zu@daiichisankyo.co.jp.,Institute of Crystallography, University of Aachen (RWTH), Aachen, Germany.,Biotechnology Center, National Chung Hsing University, Taichung City, 402, Taiwan.,Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom; Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom.,Institute of Life Science and Natural Resources, Korea University, Seoul, Republic of Korea. structures@korea.ac.kr.,Research Center for Materials Science, Nagoya University, Nagoya, Japan.,Botnar Research Centre, Oxford Biomedical Research Unit, Oxford OX3 7LD, U.K.,Nuffield Department of Medicine Research Building, Roosevelt Drive, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK. andrew.mcmichael@ndm.ox.ac.uk.,Epigenetics Discovery Performance Unit, GlaxoSmithKline R&D, Stevenage Hertfordshire SG1 2NY, United Kingdom.,Department of Life Science, POSTECH, Pohang, Gyeongbuk, Republic of Korea.,Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom.,Structural Genomics Consortium, University of Toronto, Toronto, Ontario, M5G 1L7, Canada.,Genomics Research Center, Academia Sinica, Taipei, 115, Taiwan.,Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, 66045.,Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, United States; Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109-2216, United States; Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109-2216, United States.,York Structural Biology Laboratory , Department of Chemistry , The University of York , YO10 5DD , UK.,Nuffield Department of Medicine Research Building, Roosevelt Drive, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK. geraldine.gillespie@ndm.ox.ac.uk.,Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, Kansas, 66047.,VA Tennessee Valley Healthcare System , 1310 24th Avenue S. , Nashville , Tennessee 37212 , United States.,Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Juelich, Juelich, Germany.,University of Puerto Rico at Humacao, Humacao, PR, USA.,Departments of Microbiology, 5323 Harry Hines Blvd., Dallas, Texas, 75390.,Department of Material and Biological Chemistry, Faculty of Science, Yamagata University, Yamagata, Japan.,Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas, 66506.,Molecular Medicine, Scripps Research, United States.,National Synchrotron Light Source-II, Brookhaven National Laboratory, Upton, NY 11973, USA.,Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, OX3 7FZ, UK.,T-Cell Modulation Group, Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom.,Research Service, Louis Stokes Cleveland VA Medical Center, Cleveland, OH 44106, USA.,IMCA-CAT, Hauptman-Woodward Medical Research Institute, Argonne, Illinois, 60439.,CSIRO Health and Biosecurity, Adelaide, SA, 5000, Australia.,School of Life Sciences, Anhui University, 111 Jiulong Road, Hefei, Anhui, 230601, China; Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, 111 Jiulong Road, Hefei, Anhui, 230601, China; Department of Biological and Food Engineering, Bozhou University, 2266 Tangwang Road, Bozhou, Anhui, China.,Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, 100093, China.,Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, 97006, USA.,Structural Genomics Consortium, University of Oxford, Headington, OX3 7DQ, U.K.,Oncology Chemistry, IMED Biotech Unit , AstraZeneca , Cambridge CB4 0WG , U.K.,Asubio Pharma Co., Ltd., 6-4-3 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan. Electronic address: murafuji.hidenobu.bj@daiichisankyo.co.jp.,Department of Biochemistry, National Centre of Competence in Research Chemical Biology, University of Geneva, Geneva, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-like modifier-activating enzyme 1
A, C
1015Homo sapiensMutation(s): 1 
Gene Names: UBA1 (A1S9T, UBE1)
EC: 6.2.1.45
Find proteins for P22314 (Homo sapiens)
Go to Gene View: UBA1
Go to UniProtKB:  P22314
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin
B, D
80Homo sapiensMutation(s): 0 
Gene Names: RPS27A (UBA80, UBCEP1)
Find proteins for P62979 (Homo sapiens)
Go to Gene View: RPS27A
Go to UniProtKB:  P62979
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
POP
Query on POP

Download SDF File 
Download CCD File 
A, C
PYROPHOSPHATE 2-
H2 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-L
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.14 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.212 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 104.999α = 90.00
b = 70.438β = 95.19
c = 188.851γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHASERphasing
HKL-2000data scaling
PHENIXrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01GM115568

Revision History 

  • Version 1.0: 2018-10-10
    Type: Initial release
  • Version 1.1: 2018-10-17
    Type: Data collection, Database references, Structure summary
  • Version 1.2: 2018-12-05
    Type: Data collection, Database references