4HPP | pdb_00004hpp

Crystal structure of novel glutamine synthase homolog

• PDB DOI: https://doi.org/10.2210/pdb4HPP/pdb

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


• Deposited: 2012-10-24 Released: 2012-12-26 
• Deposition Author(s): Ladner, J.E., Atanasova, V., Dolezelova, Z., Parsons, J.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.292 (Depositor), 0.291 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.204 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Starting Model: experimental

Literature

Structure and Activity of PA5508, a Hexameric Glutamine Synthetase Homologue.

Ladner, J.E., Atanasova, V., Dolezelova, Z., Parsons, J.F.

(2012) Biochemistry 51: 10121-10123

• PubMed: 23234431 
• DOI: https://doi.org/10.1021/bi3014856
• Primary Citation Related Structures: 
  4HPP


• PubMed Abstract: 
  

  The structure of PA5508 from Pseudomonas aeruginosa, a glutamine synthetase (GS) homologue, has been determined at 2.5 Å. Surprisingly, PA5508 forms single hexameric rings rather than the stacked double rings that are characteristic of GS. The C-terminal helical thong motif that links GS rings is present in PA5508; however, it is folded back toward the core of its own polypeptide, preventing it from interacting with a second ring. Interestingly, PA5508 displays a clear preference for aromatic amine substrates. Unique aspects of the structure illustrate how the enzyme is able to catalyze reactions involving bulky amines rather than ammonia.

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Organizational Affiliation: 
• Institute for Bioscience and Biotechnology Research, University of Maryland, MD, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C6  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Macromolecule Content 

• Total Structure Weight: 48.17 kDa 
• Atom Count: 3,309 
• Modeled Residue Count: 426 
• Deposited Residue Count: 443 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable glutamine synthetase	A	443	Pseudomonas aeruginosa PAO1	Mutation(s): 0  Gene Names: PA5508 EC: 6.3.1.11
UniProt
Find proteins for Q9HT65 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9HT65  Go to UniProtKB:  Q9HT65

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GLU	D [auth A]	GLUTAMIC ACID C5 H9 N O4 WHUUTDBJXJRKMK-VKHMYHEASA-N
CA	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.292 (Depositor), 0.291 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.204 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 6

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 140.01	α = 90
b = 140.01	β = 90
c = 45.03	γ = 120

Software Package:

Software Name	Purpose
CrystalClear	data collection
PHASER	phasing
REFMAC	refinement
CrystalClear	data reduction
CrystalClear	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-12-26 
Deposition Author(s): Ladner, J.E., Atanasova, V., Dolezelova, Z., Parsons, J.F.

Revision History  

• Version 1.0: 2012-12-26
  Type: Initial release
  
• Version 1.1: 2013-01-02
  Changes: Database references
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description