Cryo-EM structure of the Methanosarcina mazei glutamine synthetase (GS) with Met-Sox-P and ADP

  • Classification: LIGASE
  • Organism(s): Methanosarcina mazei Go1
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2023-07-11 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)

Experimental Data Snapshot

  • Resolution: 2.66 Å
  • Aggregation State: 3D ARRAY 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report

This is version 1.1 of the entry. See complete history


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

  • 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.

  • Organizational Affiliation

    Department of Biochemistry, 307 Research Dr., Box 3711, Duke University Medical Center, Durham, NC, 27710, USA. Maria.Schumacher@duke.edu.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glutamine synthetase
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
467Methanosarcina mazei Go1Mutation(s): 0 
Gene Names: glnA1MM_0964
Find proteins for Q8PY99 (Methanosarcina mazei (strain ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88))
Explore Q8PY99 
Go to UniProtKB:  Q8PY99
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8PY99
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on ADP

Download Ideal Coordinates CCD File 
AA [auth C]
BB [auth I]
FA [auth D]
GB [auth J]
HA [auth E]
AA [auth C],
BB [auth I],
FA [auth D],
GB [auth J],
HA [auth E],
LB [auth K],
MA [auth F],
Q [auth A],
QB [auth L],
RA [auth G],
V [auth B],
WA [auth H]
C10 H15 N5 O10 P2
P3S (Subject of Investigation/LOI)
Query on P3S

Download Ideal Coordinates CCD File 
AB [auth I]
EA [auth D]
FB [auth J]
GA [auth E]
KB [auth K]
AB [auth I],
EA [auth D],
FB [auth J],
GA [auth E],
KB [auth K],
LA [auth F],
P [auth A],
PB [auth L],
QA [auth G],
U [auth B],
VA [auth H],
Z [auth C]
C5 H13 N2 O6 P S
Query on MG

Download Ideal Coordinates CCD File 
BA [auth D]
CA [auth D]
CB [auth I]
DA [auth D]
DB [auth I]
BA [auth D],
CA [auth D],
CB [auth I],
DA [auth D],
DB [auth I],
EB [auth I],
HB [auth J],
IA [auth E],
IB [auth J],
JA [auth E],
JB [auth J],
KA [auth E],
M [auth A],
MB [auth K],
N [auth A],
NA [auth F],
NB [auth K],
O [auth A],
OA [auth F],
OB [auth K],
PA [auth F],
R [auth B],
RB [auth L],
S [auth B],
SA [auth G],
SB [auth L],
T [auth B],
TA [auth G],
TB [auth L],
UA [auth G],
W [auth C],
X [auth C],
XA [auth H],
Y [auth C],
YA [auth H],
ZA [auth H]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.66 Å
  • Aggregation State: 3D ARRAY 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35-GM130290

Revision History  (Full details and data files)

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