8TFB

Cryo-EM structure of the Methanosarcina mazei apo glutamin synthetase structure: dodecameric form

PDB DOI: https://doi.org/10.2210/pdb8TFB/pdb
EM Map EMD-41228: EMDB EMDataResource

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

Deposited: 2023-07-09 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

Method: ELECTRON MICROSCOPY
Resolution: 2.99 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.

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 Search on PubMedSearch on PubMed Central
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.

Macromolecule Content

Total Structure Weight: 634.23 kDa
Atom Count: 42,056
Modelled Residue Count: 5,316
Deposited Residue Count: 5,604
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamine synthetase	A B C D E [auth L] A, B, C, D, E [auth L], F [auth M], G [auth O], H [auth P], I [auth Q], J [auth V], K [auth X], L [auth Y]	467	Methanosarcina mazei	Mutation(s): 0 Gene Names: glnA1, MM_0964 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8PY99
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain N [auth B] SDF format, chain O [auth C] SDF format, chain P [auth D] SDF format, chain Q [auth L] SDF format, chain R [auth M] SDF format, chain S [auth O] SDF format, chain T [auth P] SDF format, chain U [auth Q] SDF format, chain V SDF format, chain W [auth X] SDF format, chain X [auth Y] MOL2 format, chain M [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth C] MOL2 format, chain P [auth D] MOL2 format, chain Q [auth L] MOL2 format, chain R [auth M] MOL2 format, chain S [auth O] MOL2 format, chain T [auth P] MOL2 format, chain U [auth Q] MOL2 format, chain V MOL2 format, chain W [auth X] MOL2 format, chain X [auth Y] mmCIF format, chain M [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth C] mmCIF format, chain P [auth D] mmCIF format, chain Q [auth L] mmCIF format, chain R [auth M] mmCIF format, chain S [auth O] mmCIF format, chain T [auth P] mmCIF format, chain U [auth Q] mmCIF format, chain V mmCIF format, chain W [auth X] mmCIF format, chain X [auth Y]	M [auth A] N [auth B] O [auth C] P [auth D] Q [auth L] M [auth A], N [auth B], O [auth C], P [auth D], Q [auth L], R [auth M], S [auth O], T [auth P], U [auth Q], V, W [auth X], X [auth Y]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth C] Focus chain P [auth D] Focus chain Q [auth L] Focus chain R [auth M] Focus chain S [auth O] Focus chain T [auth P] Focus chain U [auth Q] Focus chain V Focus chain W [auth X] Focus chain X [auth Y] Interactions & Density Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth C] Focus chain P [auth D] Focus chain Q [auth L] Focus chain R [auth M] Focus chain S [auth O] Focus chain T [auth P] Focus chain U [auth Q] Focus chain V Focus chain W [auth X] Focus chain X [auth Y]