7P1G

Structure of the P. aeruginosa ExoY-F-actin complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Mechanism of actin-dependent activation of nucleotidyl cyclase toxins from bacterial human pathogens.

Belyy, A.Merino, F.Mechold, U.Raunser, S.

(2021) Nat Commun 12: 6628-6628

  • DOI: https://doi.org/10.1038/s41467-021-26889-2
  • Primary Citation of Related Structures:  
    7P1G, 7P1H

  • PubMed Abstract: 

    Bacterial human pathogens secrete initially inactive nucleotidyl cyclases that become potent enzymes by binding to actin inside eukaryotic host cells. The underlying molecular mechanism of this activation is, however, unclear. Here, we report structures of ExoY from Pseudomonas aeruginosa and Vibrio vulnificus bound to their corresponding activators F-actin and profilin-G-actin. The structures reveal that in contrast to the apo-state, two flexible regions become ordered and interact strongly with actin. The specific stabilization of these regions results in an allosteric stabilization of the nucleotide binding pocket and thereby to an activation of the enzyme. Differences in the sequence and conformation of the actin-binding regions are responsible for the selective binding to either F- or G-actin. Other nucleotidyl cyclase toxins that bind to calmodulin rather than actin undergo a similar disordered-to-ordered transition during activation, suggesting that the allosteric activation-by-stabilization mechanism of ExoY is conserved in these enzymes, albeit the different activator.


  • Organizational Affiliation

    Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Str. 11, 44227, Dortmund, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Maltose/maltodextrin-binding periplasmic protein,Adenylate cyclase ExoYA [auth M],
D [auth K],
G [auth L],
J [auth N],
M [auth O]
773Escherichia coli K-12Pseudomonas aeruginosa PAO1
This entity is chimeric
Mutation(s): 0 
Gene Names: malEb4034JW3994exoYPA2191
UniProt
Find proteins for P0AEX9 (Escherichia coli (strain K12))
Explore P0AEX9 
Go to UniProtKB:  P0AEX9
Find proteins for Q9I1S4 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9I1S4 
Go to UniProtKB:  Q9I1S4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP0AEX9Q9I1S4
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Actin, alpha skeletal muscleB [auth C],
E [auth A],
H [auth B],
K [auth D],
N [auth E]
377Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for P68135 (Oryctolagus cuniculus)
Explore P68135 
Go to UniProtKB:  P68135
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP68135
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
PhalloidinC [auth H],
F,
I [auth G],
L [auth I],
O [auth J]
7Amanita phalloidesMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GH3
Query on GH3

Download Ideal Coordinates CCD File 
AA [auth L],
FA [auth N],
KA [auth O],
Q [auth M],
V [auth K]
3'-DEOXY-GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
QGYIFQKZZSSUCR-OBXARNEKSA-N
ADP
Query on ADP

Download Ideal Coordinates CCD File 
CA [auth B],
HA [auth D],
MA [auth E],
S [auth C],
X [auth A]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
DA [auth B],
IA [auth D],
NA [auth E],
T [auth C],
Y [auth A]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
MG
Query on MG

Download Ideal Coordinates CCD File 
BA [auth B]
EA [auth N]
GA [auth D]
JA [auth O]
LA [auth E]
BA [auth B],
EA [auth N],
GA [auth D],
JA [auth O],
LA [auth E],
P [auth M],
R [auth C],
U [auth K],
W [auth A],
Z [auth L]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
HYP
Query on HYP
C [auth H],
F,
I [auth G],
L [auth I],
O [auth J]
L-PEPTIDE LINKINGC5 H9 N O3PRO
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONSPHIRE

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Max Planck SocietyGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2021-11-17
    Type: Initial release
  • Version 1.1: 2021-12-01
    Changes: Database references