7UYG | pdb_00007uyg

Structure of the first OTU domain from Legionella pneumophila effector protein LotA

  • Classification: HYDROLASE
  • Organism(s): Legionella pneumophila
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2022-05-06 Released: 2022-12-21 
  • Deposition Author(s): Pruneda, J.N.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 
    0.221 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.195 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.196 (Depositor) 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Mechanism of Lys6 poly-ubiquitin specificity by the L. pneumophila deubiquitinase LotA.

Warren, G.D.Kitao, T.Franklin, T.G.Nguyen, J.V.Geurink, P.P.Kubori, T.Nagai, H.Pruneda, J.N.

(2023) Mol Cell 83: 105-120.e5

  • DOI: https://doi.org/10.1016/j.molcel.2022.11.022
  • Primary Citation of Related Structures:  
    7UYG, 7UYH

  • PubMed Abstract: 

    The versatility of ubiquitination to control vast domains of eukaryotic biology is due, in part, to diversification through differently linked poly-ubiquitin chains. Deciphering signaling roles for some chain types, including those linked via K6, has been stymied by a lack of specificity among the implicated regulatory proteins. Forged through strong evolutionary pressures, pathogenic bacteria have evolved intricate mechanisms to regulate host ubiquitin during infection. Herein, we identify and characterize a deubiquitinase domain of the secreted effector LotA from Legionella pneumophila that specifically regulates K6-linked poly-ubiquitin. We demonstrate the utility of LotA for studying K6 poly-ubiquitin signals. We identify the structural basis of LotA activation and poly-ubiquitin specificity and describe an essential "adaptive" ubiquitin-binding domain. Without LotA activity during infection, the Legionella-containing vacuole becomes decorated with K6 poly-ubiquitin as well as the AAA ATPase VCP/p97/Cdc48. We propose that LotA's deubiquitinase activity guards Legionella-containing vacuole components from ubiquitin-dependent extraction.


  • Organizational Affiliation
    • Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR 97239, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
LotA296Legionella pneumophilaMutation(s): 0 
Gene Names: lpg2248
UniProt
Find proteins for Q5ZTB4 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513))
Explore Q5ZTB4 
Go to UniProtKB:  Q5ZTB4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5ZTB4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IOD
Query on IOD

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
GOL
Query on GOL

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free:  0.221 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.195 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.196 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.245α = 90
b = 86.245β = 90
c = 92.304γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXrefinement
SHELXphasing
ARP/wARPmodel building
Aimlessdata scaling

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM142486

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-21
    Type: Initial release
  • Version 1.1: 2023-01-04
    Changes: Database references
  • Version 1.2: 2023-01-18
    Changes: Database references
  • Version 1.3: 2024-05-22
    Changes: Data collection