6D3V | pdb_00006d3v

Chromosomal trehalose-6-phosphate phosphatase from P. aeruginosa

• PDB DOI: https://doi.org/10.2210/pdb6D3V/pdb

• Classification: LYASE
• Organism(s): Pseudomonas sp. HMSC75E02
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-04-17 Released: 2018-05-09 
• Deposition Author(s): Hofmann, A., Cross, M., Park, S.-Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.218 (Depositor), 0.214 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.188 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Starting Model: experimental

Literature

Trehalose 6-phosphate phosphatases of Pseudomonas aeruginosa.

Cross, M., Biberacher, S., Park, S.Y., Rajan, S., Korhonen, P., Gasser, R.B., Kim, J.S., Coster, M.J., Hofmann, A.

(2018) FASEB J 32: 5470-5482

• PubMed: 29688811 
• DOI: https://doi.org/10.1096/fj.201800500R
• Primary Citation Related Structures: 
  6CJ0, 6D3V, 6D3W


• PubMed Abstract: 
  

  The opportunistic bacterium Pseudomonas aeruginosa has been recognized as an important pathogen of clinical relevance and is a leading cause of hospital-acquired infections. The presence of a glycolytic enzyme in Pseudomonas, which is known to be inhibited by trehalose 6-phosphate (T6P) in other organisms, suggests that these bacteria may be vulnerable to the detrimental effects of intracellular T6P accumulation. In the present study, we explored the structural and functional properties of trehalose 6-phosphate phosphatase (TPP) in P. aeruginosa in support of future target-based drug discovery. A survey of genomes revealed the existence of 2 TPP genes with either chromosomal or extrachromosomal location. Both TPPs were produced as recombinant proteins, and characterization of their enzymatic properties confirmed specific, magnesium-dependent catalytic hydrolysis of T6P. The 3-dimensional crystal structure of the chromosomal TPP revealed a protein dimer arising through β-sheet expansion of the individual monomers, which possess the overall fold of halo-acid dehydrogenases.-Cross, M., Biberacher, S., Park, S.-Y., Rajan, S., Korhonen, P., Gasser, R. B., Kim, J.-S., Coster, M. J., Hofmann, A. Trehalose 6-phosphate phosphatases of Pseudomonas aeruginosa.

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Organizational Affiliation: 
• Griffith Institute for Drug Discovery, Griffith University, Nathan, Queensland, Australia.
Department of Biology, Friedrich-Alexander University, Erlangen-Nuremberg, Erlangen, Germany.
Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang, Gyeongbuk, South Korea.
Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria, Australia.
Department of Chemistry, Chonnam National University, Gwangju, South Korea.
Queensland Tropical Health Alliance, Smithfield, Queensland, Australia.

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 56.68 kDa 
• Atom Count: 4,147 
• Modeled Residue Count: 502 
• Deposited Residue Count: 508 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Trehalose phosphatase	A, B	254	Pseudomonas sp. HMSC75E02	Mutation(s): 0  Gene Names: HMPREF3289_15950

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	D [auth A], I [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACY	C [auth A], H [auth B]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N
NI	E [auth A], F [auth A], G [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.218 (Depositor), 0.214 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.188 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.265	α = 90
b = 66.82	β = 119.6
c = 75.165	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-05-09 
Deposition Author(s): Hofmann, A., Cross, M., Park, S.-Y.

Revision History  

• Version 1.0: 2018-05-09
  Type: Initial release
  
• Version 1.1: 2018-10-10
  Changes: Data collection, Database references
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description