4WWM

X-ray crystal structure of Sulfolobus solfataricus Urm1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Involvement of a eukaryotic-like ubiquitin-related modifier in the proteasome pathway of the archaeon Sulfolobus acidocaldarius.

Anjum, R.S.Bray, S.M.Blackwood, J.K.Kilkenny, M.L.Coelho, M.A.Foster, B.M.Li, S.Howard, J.A.Pellegrini, L.Albers, S.V.Deery, M.J.Robinson, N.P.

(2015) Nat Commun 6: 8163-8163

  • DOI: 10.1038/ncomms9163
  • Primary Citation of Related Structures:  
    4WWM

  • PubMed Abstract: 
  • In eukaryotes, the covalent attachment of ubiquitin chains directs substrates to the proteasome for degradation. Recently, ubiquitin-like modifications have also been described in the archaeal domain of life. It has subsequently been hypothesized that ubiquitin-like proteasomal degradation might also operate in these microbes, since all archaeal species utilize homologues of the eukaryotic proteasome ...

    In eukaryotes, the covalent attachment of ubiquitin chains directs substrates to the proteasome for degradation. Recently, ubiquitin-like modifications have also been described in the archaeal domain of life. It has subsequently been hypothesized that ubiquitin-like proteasomal degradation might also operate in these microbes, since all archaeal species utilize homologues of the eukaryotic proteasome. Here we perform a structural and biochemical analysis of a ubiquitin-like modification pathway in the archaeon Sulfolobus acidocaldarius. We reveal that this modifier is homologous to the eukaryotic ubiquitin-related modifier Urm1, considered to be a close evolutionary relative of the progenitor of all ubiquitin-like proteins. Furthermore we demonstrate that urmylated substrates are recognized and processed by the archaeal proteasome, by virtue of a direct interaction with the modifier. Thus, the regulation of protein stability by Urm1 and the proteasome in archaea is likely representative of an ancient pathway from which eukaryotic ubiquitin-mediated proteolysis has evolved.


    Organizational Affiliation

    Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Uncharacterized proteinA, B91Saccharolobus solfataricus 98/2Mutation(s): 0 
Gene Names: Ssol_1261
UniProt
Find proteins for D0KRX8 (Saccharolobus solfataricus (strain 98/2))
Explore D0KRX8 
Go to UniProtKB:  D0KRX8
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 31.494α = 90
b = 65.192β = 90
c = 109.358γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling
BALBESphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United KingdomG0701443

Revision History  (Full details and data files)

  • Version 1.0: 2015-09-23
    Type: Initial release
  • Version 2.0: 2017-09-13
    Changes: Atomic model, Author supporting evidence, Derived calculations