8TFK

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

PDB DOI: https://doi.org/10.2210/pdb8TFK/pdb
EM Map EMD-41232: EMDB EMDataResource

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

Method: ELECTRON MICROSCOPY
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.

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: 643.06 kDa
Atom Count: 41,942
Modelled Residue Count: 5,280
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 A, B, C, D, E, F, G, H, I, J, K, L	467	Methanosarcina mazei Go1	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BB [auth I] SDF format, chain FA [auth D] SDF format, chain GB [auth J] SDF format, chain HA [auth E] SDF format, chain LB [auth K] SDF format, chain MA [auth F] SDF format, chain Q [auth A] SDF format, chain QB [auth L] SDF format, chain RA [auth G] SDF format, chain V [auth B] SDF format, chain WA [auth H] MOL2 format, chain AA [auth C] MOL2 format, chain BB [auth I] MOL2 format, chain FA [auth D] MOL2 format, chain GB [auth J] MOL2 format, chain HA [auth E] MOL2 format, chain LB [auth K] MOL2 format, chain MA [auth F] MOL2 format, chain Q [auth A] MOL2 format, chain QB [auth L] MOL2 format, chain RA [auth G] MOL2 format, chain V [auth B] MOL2 format, chain WA [auth H] mmCIF format, chain AA [auth C] mmCIF format, chain BB [auth I] mmCIF format, chain FA [auth D] mmCIF format, chain GB [auth J] mmCIF format, chain HA [auth E] mmCIF format, chain LB [auth K] mmCIF format, chain MA [auth F] mmCIF format, chain Q [auth A] mmCIF format, chain QB [auth L] mmCIF format, chain RA [auth G] mmCIF format, chain V [auth B] mmCIF format, chain WA [auth H]	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]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain AA [auth C] Focus chain BB [auth I] Focus chain FA [auth D] Focus chain GB [auth J] Focus chain HA [auth E] Focus chain LB [auth K] Focus chain MA [auth F] Focus chain Q [auth A] Focus chain QB [auth L] Focus chain RA [auth G] Focus chain V [auth B] Focus chain WA [auth H] Interactions & Density Focus chain AA [auth C] Focus chain BB [auth I] Focus chain FA [auth D] Focus chain GB [auth J] Focus chain HA [auth E] Focus chain LB [auth K] Focus chain MA [auth F] Focus chain Q [auth A] Focus chain QB [auth L] Focus chain RA [auth G] Focus chain V [auth B] Focus chain WA [auth H]
P3S (Subject of Investigation/LOI) Query on P3S Download Ideal Coordinates CCD File SDF format, chain AB [auth I] SDF format, chain EA [auth D] SDF format, chain FB [auth J] SDF format, chain GA [auth E] SDF format, chain KB [auth K] SDF format, chain LA [auth F] SDF format, chain P [auth A] SDF format, chain PB [auth L] SDF format, chain QA [auth G] SDF format, chain U [auth B] SDF format, chain VA [auth H] SDF format, chain Z [auth C] MOL2 format, chain AB [auth I] MOL2 format, chain EA [auth D] MOL2 format, chain FB [auth J] MOL2 format, chain GA [auth E] MOL2 format, chain KB [auth K] MOL2 format, chain LA [auth F] MOL2 format, chain P [auth A] MOL2 format, chain PB [auth L] MOL2 format, chain QA [auth G] MOL2 format, chain U [auth B] MOL2 format, chain VA [auth H] MOL2 format, chain Z [auth C] mmCIF format, chain AB [auth I] mmCIF format, chain EA [auth D] mmCIF format, chain FB [auth J] mmCIF format, chain GA [auth E] mmCIF format, chain KB [auth K] mmCIF format, chain LA [auth F] mmCIF format, chain P [auth A] mmCIF format, chain PB [auth L] mmCIF format, chain QA [auth G] mmCIF format, chain U [auth B] mmCIF format, chain VA [auth H] mmCIF format, chain Z [auth C]	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]	L-METHIONINE-S-SULFOXIMINE PHOSPHATE C₅ H₁₃ N₂ O₆ P S QQFOFBSCSWFFPB-NMAPHRJESA-N		Interactions Focus chain AB [auth I] Focus chain EA [auth D] Focus chain FB [auth J] Focus chain GA [auth E] Focus chain KB [auth K] Focus chain LA [auth F] Focus chain P [auth A] Focus chain PB [auth L] Focus chain QA [auth G] Focus chain U [auth B] Focus chain VA [auth H] Focus chain Z [auth C] Interactions & Density Focus chain AB [auth I] Focus chain EA [auth D] Focus chain FB [auth J] Focus chain GA [auth E] Focus chain KB [auth K] Focus chain LA [auth F] Focus chain P [auth A] Focus chain PB [auth L] Focus chain QA [auth G] Focus chain U [auth B] Focus chain VA [auth H] Focus chain Z [auth C]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain CA [auth D] SDF format, chain CB [auth I] SDF format, chain DA [auth D] SDF format, chain EB [auth I] SDF format, chain HB [auth J] SDF format, chain IA [auth E] SDF format, chain IB [auth J] SDF format, chain JA [auth E] SDF format, chain JB [auth J] SDF format, chain KA [auth E] SDF format, chain M [auth A] SDF format, chain MB [auth K] SDF format, chain N [auth A] SDF format, chain NA [auth F] SDF format, chain NB [auth K] SDF format, chain O [auth A] SDF format, chain OA [auth F] SDF format, chain OB [auth K] SDF format, chain PA [auth F] SDF format, chain R [auth B] SDF format, chain RB [auth L] SDF format, chain S [auth B] SDF format, chain SA [auth G] SDF format, chain SB [auth L] SDF format, chain T [auth B] SDF format, chain TA [auth G] SDF format, chain TB [auth L] SDF format, chain UA [auth G] SDF format, chain W [auth C] SDF format, chain X [auth C] SDF format, chain XA [auth H] SDF format, chain Y [auth C] SDF format, chain YA [auth H] SDF format, chain ZA [auth H] SDF format, chain DB [auth I] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain CB [auth I] MOL2 format, chain DA [auth D] MOL2 format, chain EB [auth I] MOL2 format, chain HB [auth J] MOL2 format, chain IA [auth E] MOL2 format, chain IB [auth J] MOL2 format, chain JA [auth E] MOL2 format, chain JB [auth J] MOL2 format, chain KA [auth E] MOL2 format, chain M [auth A] MOL2 format, chain MB [auth K] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth F] MOL2 format, chain NB [auth K] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth F] MOL2 format, chain OB [auth K] MOL2 format, chain PA [auth F] MOL2 format, chain R [auth B] MOL2 format, chain RB [auth L] MOL2 format, chain S [auth B] MOL2 format, chain SA [auth G] MOL2 format, chain SB [auth L] MOL2 format, chain T [auth B] MOL2 format, chain TA [auth G] MOL2 format, chain TB [auth L] MOL2 format, chain UA [auth G] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] MOL2 format, chain XA [auth H] MOL2 format, chain Y [auth C] MOL2 format, chain YA [auth H] MOL2 format, chain ZA [auth H] MOL2 format, chain DB [auth I] mmCIF format, chain BA [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain CB [auth I] mmCIF format, chain DA [auth D] mmCIF format, chain EB [auth I] mmCIF format, chain HB [auth J] mmCIF format, chain IA [auth E] mmCIF format, chain IB [auth J] mmCIF format, chain JA [auth E] mmCIF format, chain JB [auth J] mmCIF format, chain KA [auth E] mmCIF format, chain M [auth A] mmCIF format, chain MB [auth K] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth F] mmCIF format, chain NB [auth K] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth F] mmCIF format, chain OB [auth K] mmCIF format, chain PA [auth F] mmCIF format, chain R [auth B] mmCIF format, chain RB [auth L] mmCIF format, chain S [auth B] mmCIF format, chain SA [auth G] mmCIF format, chain SB [auth L] mmCIF format, chain T [auth B] mmCIF format, chain TA [auth G] mmCIF format, chain TB [auth L] mmCIF format, chain UA [auth G] mmCIF format, chain W [auth C] mmCIF format, chain X [auth C] mmCIF format, chain XA [auth H] mmCIF format, chain Y [auth C] mmCIF format, chain YA [auth H] mmCIF format, chain ZA [auth H] mmCIF format, chain DB [auth I]	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]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain CA [auth D] Focus chain CB [auth I] Focus chain DA [auth D] Focus chain DB [auth I] Focus chain EB [auth I] Focus chain HB [auth J] Focus chain IA [auth E] Focus chain IB [auth J] Focus chain JA [auth E] Focus chain JB [auth J] Focus chain KA [auth E] Focus chain M [auth A] Focus chain MB [auth K] Focus chain N [auth A] Focus chain NA [auth F] Focus chain NB [auth K] Focus chain O [auth A] Focus chain OA [auth F] Focus chain OB [auth K] Focus chain PA [auth F] Focus chain R [auth B] Focus chain RB [auth L] Focus chain S [auth B] Focus chain SA [auth G] Focus chain SB [auth L] Focus chain T [auth B] Focus chain TA [auth G] Focus chain TB [auth L] Focus chain UA [auth G] Focus chain W [auth C] Focus chain X [auth C] Focus chain XA [auth H] Focus chain Y [auth C] Focus chain YA [auth H] Focus chain ZA [auth H] Interactions & Density Focus chain BA [auth D] Focus chain CA [auth D] Focus chain CB [auth I] Focus chain DA [auth D] Focus chain DB [auth I] Focus chain EB [auth I] Focus chain HB [auth J] Focus chain IA [auth E] Focus chain IB [auth J] Focus chain JA [auth E] Focus chain JB [auth J] Focus chain KA [auth E] Focus chain M [auth A] Focus chain MB [auth K] Focus chain N [auth A] Focus chain NA [auth F] Focus chain NB [auth K] Focus chain O [auth A] Focus chain OA [auth F] Focus chain OB [auth K] Focus chain PA [auth F] Focus chain R [auth B] Focus chain RB [auth L] Focus chain S [auth B] Focus chain SA [auth G] Focus chain SB [auth L] Focus chain T [auth B] Focus chain TA [auth G] Focus chain TB [auth L] Focus chain UA [auth G] Focus chain W [auth C] Focus chain X [auth C] Focus chain XA [auth H] Focus chain Y [auth C] Focus chain YA [auth H] Focus chain ZA [auth H]