8UFJ

Structure of M. mazei GS(R167L-A168G) apo form

• PDB DOI: https://doi.org/10.2210/pdb8UFJ/pdb

• Classification: LIGASE
• Organism(s): Methanosarcina mazei Go1
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2023-10-04 Released: 2023-11-15 
• Deposition Author(s): Schumacher, M.A.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 0.222 
• R-Value Work: 0.190 
• R-Value Observed: 0.191 

Starting Model: experimental

Literature

M. mazei glutamine synthetase and glutamine synthetase-GlnK1 structures reveal enzyme regulation by oligomer modulation.

Schumacher, M.A., Salinas, R., Travis, B.A., Singh, R.R., Lent, N.

(2023) Nat Commun 14: 7375-7375

• PubMed: 37968329 
• DOI: https://doi.org/10.1038/s41467-023-43243-w
• Primary Citation of Related Structures:  
  8TFB, 8TFC, 8TFK, 8TGE, 8UFJ


• PubMed Abstract: 
  

  Glutamine synthetases (GS) play central roles in cellular nitrogen assimilation. Although GS active-site formation requires the oligomerization of just two GS subunits, all GS form large, multi-oligomeric machines. Here we describe a structural dissection of the archaeal Methanosarcina mazei (Mm) GS and its regulation. We show that Mm GS forms unstable dodecamers. Strikingly, we show this Mm GS oligomerization property is leveraged for a unique mode of regulation whereby labile Mm GS hexamers are stabilized by binding the nitrogen regulatory protein, GlnK1. Our GS-GlnK1 structure shows that GlnK1 functions as molecular glue to affix GS hexamers together, stabilizing formation of GS active-sites. These data, therefore, reveal the structural basis for a unique form of enzyme regulation by oligomer modulation.

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Organizational Affiliation: 

Department of Biochemistry, 307 Research Dr., Box 3711, Duke University Medical Center, Durham, NC, 27710, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Dihedral - D6  (Explore in 3D)
Global Stoichiometry: Homo 12-mer - A12 

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

Macromolecule Content

• Total Structure Weight: 158.46 kDa 
• Atom Count: 10,699 
• Modelled Residue Count: 1,330 
• Deposited Residue Count: 1,401 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamine synthetase	A, B, C	467	Methanosarcina mazei Go1	Mutation(s): 2  Gene Names: glnA1 EC: 6.3.1.2
UniProt
Find proteins for Q8PY99 (Methanosarcina mazei (strain ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88)) Explore Q8PY99  Go to UniProtKB:  Q8PY99

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG (Subject of Investigation/LOI)	D [auth A], E [auth A], F [auth B], G [auth B], H [auth C], I [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 0.222 
• R-Value Work: 0.190 
• R-Value Observed: 0.191 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 137.264	α = 90
b = 167.546	β = 90
c = 176.922	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-11-15 
Deposition Author(s): Schumacher, M.A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35-GM130290

Revision History  

• Version 1.0: 2023-11-15
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Database references