6O83

S. pombe ubiquitin E1~ubiquitin-AMP tetrahedral intermediate mimic


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.153 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural basis for adenylation and thioester bond formation in the ubiquitin E1.

Hann, Z.S.Ji, C.Olsen, S.K.Lu, X.Lux, M.C.Tan, D.S.Lima, C.D.

(2019) Proc.Natl.Acad.Sci.USA 116: 15475-15484

  • DOI: 10.1073/pnas.1905488116
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The ubiquitin (Ub) and Ub-like (Ubl) protein-conjugation cascade is initiated by E1 enzymes that catalyze Ub/Ubl activation through C-terminal adenylation, thioester bond formation with an E1 catalytic cysteine, and thioester bond transfer to Ub/Ubl ...

    The ubiquitin (Ub) and Ub-like (Ubl) protein-conjugation cascade is initiated by E1 enzymes that catalyze Ub/Ubl activation through C-terminal adenylation, thioester bond formation with an E1 catalytic cysteine, and thioester bond transfer to Ub/Ubl E2 conjugating enzymes. Each of these reactions is accompanied by conformational changes of the E1 domain that contains the catalytic cysteine (Cys domain). Open conformations of the Cys domain are associated with adenylation and thioester transfer to E2s, while a closed conformation is associated with pyrophosphate release and thioester bond formation. Several structures are available for Ub E1s, but none has been reported in the open state before pyrophosphate release or in the closed state. Here, we describe the structures of Schizosaccharomyces pombe Ub E1 in these two states, captured using semisynthetic Ub probes. In the first, with a Ub-adenylate mimetic (Ub-AMSN) bound, the E1 is in an open conformation before release of pyrophosphate. In the second, with a Ub-vinylsulfonamide (Ub-AVSN) bound covalently to the catalytic cysteine, the E1 is in a closed conformation required for thioester bond formation. These structures provide further insight into Ub E1 adenylation and thioester bond formation. Conformational changes that accompany Cys-domain rotation are conserved for SUMO and Ub E1s, but changes in Ub E1 involve additional surfaces as mutational and biochemical analysis of residues within these surfaces alter Ub E1 activities.


    Organizational Affiliation

    Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, NY 10065.,Chemical Biology Program, Sloan Kettering Institute, New York, NY 10065.,Howard Hughes Medical Institute, New York, NY, 10065.,Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, NY 10065; tand@mskcc.org limac@mskcc.org.,Structural Biology Program, Sloan Kettering Institute, New York, NY 10065.,Structural Biology Program, Sloan Kettering Institute, New York, NY 10065; tand@mskcc.org limac@mskcc.org.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-activating enzyme E1 1
A, C
1001Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 0 
Gene Names: ptr3
EC: 6.2.1.45
Find proteins for O94609 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  O94609
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-60S ribosomal protein L40
B, D
75Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 0 
Gene Names: uep1 (ubi2)
Find proteins for P0CH07 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  P0CH07
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, C
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MPD
Query on MPD

Download SDF File 
Download CCD File 
A, C
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
TRS
Query on TRS

Download SDF File 
Download CCD File 
A, C
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
VMX
Query on VMX

Download SDF File 
Download CCD File 
A, C
5'-{[(3-aminopropyl)sulfonyl]amino}-5'-deoxyadenosine
C13 H21 N7 O5 S
GCNSCCULRVBOML-QYVSTXNMSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.153 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.203 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 122.575α = 90.00
b = 150.522β = 90.00
c = 172.776γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHENIXphasing
HKL-2000data scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2019-03-08 
  • Released Date: 2019-06-19 
  • Deposition Author(s): Hann, Z.S., Lima, C.D.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM079196
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM118080
Howard Hughes Medical Institute (HHMI)United States--
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM100477
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesP30CA008748

Revision History 

  • Version 1.0: 2019-06-19
    Type: Initial release
  • Version 1.1: 2019-07-10
    Type: Data collection, Database references
  • Version 1.2: 2019-08-14
    Type: Data collection, Database references
  • Version 1.3: 2019-11-20
    Type: Author supporting evidence