6WTG

SdeA DUB Domain in complex with Ubiquitin

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.63 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Insights into Ubiquitin Product Release in Hydrolysis Catalyzed by the Bacterial Deubiquitinase SdeA.

Sheedlo, M.J., Kenny, S., Podkorytov, I.S., Brown, K., Ma, J., Iyer, S., Hewitt, C.S., Arbough, T., Mikhailovskii, O., Flaherty, D.P., Wilson, M.A., Skrynnikov, N.R., Das, C.

(2021) Biochemistry 60: 584-596

  • DOI: 10.1021/acs.biochem.0c00760
  • Primary Citation of Related Structures:  
    6WTG

  • PubMed Abstract: 

    • We report the co-crystal structure of the (catalytic Cys)-to-Ala mutant of the deubiquitinase domain of the Legionella pneumophila effector SdeA (SdeA DUB ) with its ubiquitin (Ub) product. Most of the intermolecular interactions are preserved in this product-bound structure compared to that of the previously characterized complex of SdeA DUB with the suicide inhibitor ubiquitin vinylmethyl ester (Ub-VME), whose structure models the acyl-enzyme thioester intermediate ...

    We report the co-crystal structure of the (catalytic Cys)-to-Ala mutant of the deubiquitinase domain of the Legionella pneumophila effector SdeA (SdeA DUB ) with its ubiquitin (Ub) product. Most of the intermolecular interactions are preserved in this product-bound structure compared to that of the previously characterized complex of SdeA DUB with the suicide inhibitor ubiquitin vinylmethyl ester (Ub-VME), whose structure models the acyl-enzyme thioester intermediate. Nuclear magnetic resonance (NMR) titration studies show a chemical shift perturbation pattern that suggests that the same interactions also exist in solution. Isothermal titration calorimetry and NMR titration data reveal that the affinity of wild-type (WT) SdeA DUB for Ub is significantly lower than that of the Cys-to-Ala mutant. This is potentially due to repulsive interaction between the thiolate ion of the catalytic Cys residue in WT SdeA DUB and the carboxylate group of the C-terminal Gly76 residue in Ub. In the context of SdeA DUB catalysis, this electrostatic repulsion arises after the hydrolysis of the scissile isopeptide bond in the acyl-enzyme intermediate and the consequent formation of the C-terminal carboxylic group in the Ub fragment. We hypothesize that this electrostatic repulsion may expedite the release of the Ub product by SdeA DUB . We note that similar repulsive interactions may also occur in other deubiquitinases and hydrolases of ubiquitin-like protein modifiers and may constitute a fairly general mechanism of product release within this family. This is a potentially important feature for a family of enzymes that form extensive protein-protein interactions during enzyme-substrate engagement.

    Related Citations: 
    • Structural basis of substrate recognition by a bacterial deubiquitinase important for dynamics of phagosome ubiquitination.
      Sheedlo, M.J., Qiu, J., Tan, Y., Paul, L.N., Luo, Z.Q., Das, C.
      (2015) Proc Natl Acad Sci U S A 112: 15090
    Organizational Affiliation: 

    Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitinating/deubiquitinating enzyme SdeAA193Legionella pneumophila subsp. pneumophila str. Philadelphia 1Mutation(s): 1 
Gene Names: sdeA, lpg2157
EC: 3.4.22 (PDB Primary Data), 2.3.2 (PDB Primary Data), 2.4.2.31 (PDB Primary Data)
UniProt
Find proteins for Q5ZTK4 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513))
Explore Q5ZTK4 
Go to UniProtKB:  Q5ZTK4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5ZTK4
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
UbiquitinB [auth D]76Homo sapiensMutation(s): 0 
Gene Names: UBC
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG48 (Homo sapiens)
Explore P0CG48 
Go to UniProtKB:  P0CG48
PHAROS:  P0CG48
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0CG48
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.63 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 31.257α = 90
b = 43.208β = 90
c = 195.964γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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View more in-depth experimental data

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States5R01GM126296-03
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1T32GM132024-01

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-03
    Type: Initial release
  • Version 1.1: 2021-03-17
    Changes: Database references