6GZS

Structure of Chlamydia trachomatis effector protein ChlaDUB1 bound to ubiquitin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

A Chlamydia effector combining deubiquitination and acetylation activities induces Golgi fragmentation.

Pruneda, J.N.Bastidas, R.J.Bertsoulaki, E.Swatek, K.N.Santhanam, B.Clague, M.J.Valdivia, R.H.Urbe, S.Komander, D.

(2018) Nat Microbiol 3: 1377-1384

  • DOI: 10.1038/s41564-018-0271-y
  • Primary Citation of Related Structures:  
    6GZT, 6GZS, 6GZU

  • PubMed Abstract: 
  • Pathogenic bacteria are armed with potent effector proteins that subvert host signalling processes during infection 1 . The activities of bacterial effectors and their associated roles within the host cell are often poorly understood, particul ...

    Pathogenic bacteria are armed with potent effector proteins that subvert host signalling processes during infection 1 . The activities of bacterial effectors and their associated roles within the host cell are often poorly understood, particularly for Chlamydia trachomatis 2 , a World Health Organization designated neglected disease pathogen. We identify and explain remarkable dual Lys63-deubiquitinase (DUB) and Lys-acetyltransferase activities in the Chlamydia effector ChlaDUB1. Crystal structures capturing intermediate stages of each reaction reveal how the same catalytic centre of ChlaDUB1 can facilitate such distinct processes, and enable the generation of mutations that uncouple the two activities. Targeted Chlamydia mutant strains allow us to link the DUB activity of ChlaDUB1 and the related, dedicated DUB ChlaDUB2 to fragmentation of the host Golgi apparatus, a key process in Chlamydia infection for which effectors have remained elusive. Our work illustrates the incredible versatility of bacterial effector proteins, and provides important insights towards understanding Chlamydia pathogenesis.


    Organizational Affiliation

    Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Cambridge, UK. dk@mrc-lmb.cam.ac.uk.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Deubiquitinase and deneddylase Dub1 A273Chlamydia trachomatis 434/BuMutation(s): 0 
Gene Names: cdu1CTL0247
EC: 3.4.22
Find proteins for B0B9A0 (Chlamydia trachomatis serovar L2 (strain 434/Bu / ATCC VR-902B))
Explore B0B9A0 
Go to UniProtKB:  B0B9A0
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Polyubiquitin-B B75Homo sapiensMutation(s): 0 
Gene Names: UBB
Find proteins for P0CG47 (Homo sapiens)
Explore P0CG47 
Go to UniProtKB:  P0CG47
NIH Common Fund Data Resources
PHAROS:  P0CG47
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
AYE
Query on AYE

Download Ideal Coordinates CCD File 
B
prop-2-en-1-amine
C3 H7 N
VVJKKWFAADXIJK-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.798α = 90
b = 55.768β = 93.57
c = 58.574γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
AutoSolphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United KingdomU105192732
European Research CouncilUnited Kingdom724804

Revision History 

  • Version 1.0: 2018-11-14
    Type: Initial release
  • Version 1.1: 2018-12-05
    Changes: Data collection, Database references