3FY3 | pdb_00003fy3

Crystal structure of truncated hemolysin A from P. mirabilis

• PDB DOI: https://doi.org/10.2210/pdb3FY3/pdb

• Classification: TOXIN
• Organism(s): Proteus mirabilis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-01-21 Released: 2009-06-02 
• Deposition Author(s): Weaver, T.M., Thompson, J.R., Bailey, L.J., Wawrzyn, G.T., Hocking, J.M., Howard, D.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.203 (Depositor), 0.236 (DCC) 
• R-Value Work: 
  0.149 (Depositor), 0.218 (DCC) 
• R-Value Observed: 
  0.151 (Depositor) 

Starting Model: experimental

Literature

Structural and functional studies of truncated hemolysin A from Proteus mirabilis.

Weaver, T.M., Hocking, J.M., Bailey, L.J., Wawrzyn, G.T., Howard, D.R., Sikkink, L.A., Ramirez-Alvarado, M., Thompson, J.R.

(2009) J Biological Chem 284: 22297-22309

• PubMed: 19494116 
• DOI: https://doi.org/10.1074/jbc.M109.014431
• Primary Citation Related Structures: 
  3FY3


• PubMed Abstract: 
  

  In this study we analyzed the structure and function of a truncated form of hemolysin A (HpmA265) from Proteus mirabilis using a series of functional and structural studies. Hemolysin A belongs to the two-partner secretion pathway. The two-partner secretion pathway has been identified as the most common protein secretion pathway among Gram-negative bacteria. Currently, the mechanism of action for the two-partner hemolysin members is not fully understood. In this study, hemolysis experiments revealed a unidirectional, cooperative, biphasic activity profile after full-length, inactive hemolysin A was seeded with truncated hemolysin A. We also solved the first x-ray structure of a TpsA hemolysin. The truncated hemolysin A formed a right-handed parallel beta-helix with three adjoining segments of anti-parallel beta-sheet. A CXXC disulfide bond, four buried solvent molecules, and a carboxyamide ladder were all located at the third complete beta-helix coil. Replacement of the CXXC motif led to decreased activity and stability according to hemolysis and CD studies. Furthermore, the crystal structure revealed a sterically compatible, dry dimeric interface formed via anti-parallel beta-sheet interactions between neighboring beta-helix monomers. Laser scanning confocal microscopy further supported the unidirectional interconversion of full-length hemolysin A. From these results, a model has been proposed, where cooperative, beta-strand interactions between HpmA265 and neighboring full-length hemolysin A molecules, facilitated in part by the highly conserved CXXC pattern, account for the template-assisted hemolysis.

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Organizational Affiliation: 
• Departments of Chemistry, La Crosse, Wisconsin 54601.
Biology, University Wisconsin-La Crosse, La Crosse, Wisconsin 54601.
the Departments of Biochemistry and Molecular Biology, Rochester, Minnesota 55905.
Physiology and Biomedical Imaging, College of Medicine, Mayo Clinic, Rochester, Minnesota 55905.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 24.65 kDa 
• Atom Count: 1,936 
• Modeled Residue Count: 234 
• Deposited Residue Count: 236 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemolysin	A	236	Proteus mirabilis	Mutation(s): 0  Gene Names: hpmA
UniProt
Find proteins for P16466 (Proteus mirabilis) Explore P16466  Go to UniProtKB:  P16466

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.203 (Depositor), 0.236 (DCC) 
• R-Value Work:  0.149 (Depositor), 0.218 (DCC) 
• R-Value Observed: 0.151 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.273	α = 90
b = 119.528	β = 90
c = 34.199	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-06-02 
Deposition Author(s): Weaver, T.M., Thompson, J.R., Bailey, L.J., Wawrzyn, G.T., Hocking, J.M., Howard, D.R.

Revision History  

• Version 1.0: 2009-06-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-11-20
  Changes: Structure summary