6O82

S. pombe ubiquitin E1 complex with a ubiquitin-AMP mimic

  • Classification: LIGASE/PROTEIN BINDING
  • Organism(s): Schizosaccharomyces pombe 972h-
  • Expression System: Escherichia coli
  • Mutation(s): Yes 

  • Deposited: 2019-03-08 Released: 2019-06-19 
  • Deposition Author(s): Olsen, S.K., Lima, C.D.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Howard Hughes Medical Institute (HHMI), National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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 U S A 116: 15475-15484

  • DOI: 10.1073/pnas.1905488116
  • Primary Citation of Related Structures:  
    6O82, 6O83

  • 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 E2 conjugating enzymes ...

    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

    Howard Hughes Medical Institute, New York, NY, 10065.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-activating enzyme E1 1A, C1001Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: ptr3SPBC1604.21cSPBC211.09
EC: 6.2.1.45
UniProt
Find proteins for O94609 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore O94609 
Go to UniProtKB:  O94609
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-60S ribosomal protein L40B, D76Schizosaccharomyces pombe 972h-Mutation(s): 1 
Gene Names: uep1ubi2SPAC1805.12c
UniProt
Find proteins for P0CH07 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore P0CH07 
Go to UniProtKB:  P0CH07
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
JZU (Subject of Investigation/LOI)
Query on JZU

Download Ideal Coordinates CCD File 
O [auth B], V [auth D]5'-deoxy-5'-(sulfamoylamino)adenosine
C10 H15 N7 O5 S
RCHUICYCIUKUIY-KQYNXXCUSA-N
 Ligand Interaction
POP (Subject of Investigation/LOI)
Query on POP

Download Ideal Coordinates CCD File 
G [auth A], H [auth A], R [auth C]PYROPHOSPHATE 2-
H2 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-L
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], S [auth C], T [auth C]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
N [auth A], U [auth C]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
E [auth A], F [auth A], P [auth C], Q [auth C]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 182.061α = 90
b = 114.616β = 90
c = 125.967γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


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  (Full details and data files)

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