6E8M

Legionella Longbeachae LeSH (Llo2327) bound to the human DnaJ-A1 pTyr381 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.61 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Identification and characterization of a large family of superbinding bacterial SH2 domains.

Kaneko, T.Stogios, P.J.Ruan, X.Voss, C.Evdokimova, E.Skarina, T.Chung, A.Liu, X.Li, L.Savchenko, A.Ensminger, A.W.Li, S.S.

(2018) Nat Commun 9: 4549-4549

  • DOI: https://doi.org/10.1038/s41467-018-06943-2
  • Primary Citation of Related Structures:  
    6E8H, 6E8I, 6E8K, 6E8M

  • PubMed Abstract: 

    Src homology 2 (SH2) domains play a critical role in signal transduction in mammalian cells by binding to phosphorylated Tyr (pTyr). Apart from a few isolated cases in viruses, no functional SH2 domain has been identified to date in prokaryotes. Here we identify 93 SH2 domains from Legionella that are distinct in sequence and specificity from mammalian SH2 domains. The bacterial SH2 domains are not only capable of binding proteins or peptides in a Tyr phosphorylation-dependent manner, some bind pTyr itself with micromolar affinities, a property not observed for mammalian SH2 domains. The Legionella SH2 domains feature the SH2 fold and a pTyr-binding pocket, but lack a specificity pocket found in a typical mammalian SH2 domain for recognition of sequences flanking the pTyr residue. Our work expands the boundary of phosphotyrosine signalling to prokaryotes, suggesting that some bacterial effector proteins have acquired pTyr-superbinding characteristics to facilitate bacterium-host interactions.


  • Organizational Affiliation

    Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 5C1, Canada.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
LeSH (Llo2327)169Legionella longbeachae NSW150Mutation(s): 0 
Gene Names: LLO_2327
UniProt
Find proteins for D3HJY4 (Legionella longbeachae serogroup 1 (strain NSW150))
Explore D3HJY4 
Go to UniProtKB:  D3HJY4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD3HJY4
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DnaJ-A1 pTyr381 peptide13Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P31689 (Homo sapiens)
Explore P31689 
Go to UniProtKB:  P31689
PHAROS:  P31689
GTEx:  ENSG00000086061 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP31689
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PTR
Query on PTR
B
L-PEPTIDE LINKINGC9 H12 N O6 PTYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.61 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.199 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.9α = 90
b = 64.71β = 90
c = 67.85γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
Auto-Rickshawphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-11-14
    Type: Initial release
  • Version 1.1: 2019-12-04
    Changes: Author supporting evidence
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2023-11-15
    Changes: Data collection