4BJ4 | pdb_00004bj4

Structure of Pseudomonas aeruginosa amidase Ampdh2

• PDB DOI: https://doi.org/10.2210/pdb4BJ4/pdb

• Classification: HYDROLASE
• Organism(s): Pseudomonas aeruginosa PAO1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-04-16 Released: 2013-07-24 
• Deposition Author(s): Martinez-Caballero, C.S., Carrasco-Lopez, C., Artola-Recolons, C., Hermoso, J.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free: 
  0.201 (Depositor), 0.201 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.173 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

Starting Model: experimental

Literature

Reaction Products and the X-Ray Structure of Ampdh2, a Virulence Determinant of Pseudomonas Aeruginosa.

Martinez-Caballero, S., Lee, M., Artola-Recolons, C., Carrasco-Lopez, C., Hesek, D., Spink, E.E., Lastochkin, E., Zhang, W., Hellman, L.M., Boggess, B., Mobashery, S., Hermoso, J.A.

(2013) J Am Chem Soc 135: 10318

• PubMed: 23819763 
• DOI: https://doi.org/10.1021/ja405464b
• Primary Citation Related Structures: 
  4BJ4, 4BOL, 4BPA


• PubMed Abstract: 
  

  The zinc protease AmpDh2 is a virulence determinant of Pseudomonas aeruginosa, a problematic human pathogen. The mechanism of how the protease manifests virulence is not known, but it is known that it turns over the bacterial cell wall. The reaction of AmpDh2 with the cell wall was investigated, and nine distinct turnover products were characterized by LC/MS/MS. The enzyme turns over both the cross-linked and noncross-linked cell wall. Three high-resolution X-ray structures, the apo enzyme and two complexes with turnover products, were solved. The X-ray structures show how the dimeric protein interacts with the inner leaflet of the bacterial outer membrane and that the two monomers provide a more expansive surface for recognition of the cell wall. This binding surface can accommodate the 3D solution structure of the cross-linked cell wall.

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Organizational Affiliation: 
• Department of Crystallography and Structural Biology, Inst. Química-Física "Rocasolano", CSIC, Serrano 119, 28006 Madrid, Spain.
Department of Chemistry and Biochemistry, Nieuwland Science Hall, Notre Dame, Indiana 46556, United States.

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: 55.18 kDa 
• Atom Count: 4,799 
• Modeled Residue Count: 492 
• Deposited Residue Count: 492 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AMPDH2	A, B	246	Pseudomonas aeruginosa PAO1	Mutation(s): 0  EC: 3.5.1.28
UniProt
Find proteins for Q9HT86 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9HT86  Go to UniProtKB:  Q9HT86

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FLC	C [auth A]	CITRATE ANION C6 H5 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free:  0.201 (Depositor), 0.201 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.173 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.759	α = 90
b = 100.421	β = 90
c = 104.26	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-07-24 
Deposition Author(s): Martinez-Caballero, C.S., Carrasco-Lopez, C., Artola-Recolons, C., Hermoso, J.A.

Revision History  

• Version 1.0: 2013-07-24
  Type: Initial release
  
• Version 1.1: 2013-07-31
  Changes: Database references
• Version 1.2: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description