8OOO

Glutamine synthetase from Methanothermococcus thermolithotrophicus in complex with 2-oxoglutarate and MgATP at 2.15 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.183 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Differences in regulation mechanisms of glutamine synthetases from methanogenic archaea unveiled by structural investigations.

Muller, M.C.Lemaire, O.N.Kurth, J.M.Welte, C.U.Wagner, T.

(2024) Commun Biol 7: 111-111

  • DOI: https://doi.org/10.1038/s42003-023-05726-w
  • Primary Citation of Related Structures:  
    8OOL, 8OON, 8OOO, 8OOQ, 8OOW, 8OOX, 8OOZ

  • PubMed Abstract: 

    Glutamine synthetases (GS) catalyze the ATP-dependent ammonium assimilation, the initial step of nitrogen acquisition that must be under tight control to fit cellular needs. While their catalytic mechanisms and regulations are well-characterized in bacteria and eukaryotes, only limited knowledge exists in archaea. Here, we solved two archaeal GS structures and unveiled unexpected differences in their regulatory mechanisms. GS from Methanothermococcus thermolithotrophicus is inactive in its resting state and switched on by 2-oxoglutarate, a sensor of cellular nitrogen deficiency. The enzyme activation overlays remarkably well with the reported cellular concentration for 2-oxoglutarate. Its binding to an allosteric pocket reconfigures the active site through long-range conformational changes. The homolog from Methermicoccus shengliensis does not harbor the 2-oxoglutarate binding motif and, consequently, is 2-oxoglutarate insensitive. Instead, it is directly feedback-inhibited through glutamine recognition by the catalytic Asp50'-loop, a mechanism common to bacterial homologs, but absent in M. thermolithotrophicus due to residue substitution. Analyses of residue conservation in archaeal GS suggest that both regulations are widespread and not mutually exclusive. While the effectors and their binding sites are surprisingly different, the molecular mechanisms underlying their mode of action on GS activity operate on the same molecular determinants in the active site.


  • Organizational Affiliation

    Microbial Metabolism Research Group, Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glutamine synthetase from Methanothermococcus thermolithotrophicus
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
448Methanothermococcus thermolithotrophicus DSM 2095Mutation(s): 0 
EC: 6.3.1.2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP (Subject of Investigation/LOI)
Query on ATP

Download Ideal Coordinates CCD File 
AA [auth B]
BC [auth L]
FA [auth C]
FB [auth G]
IB [auth H]
AA [auth B],
BC [auth L],
FA [auth C],
FB [auth G],
IB [auth H],
MA [auth D],
MB [auth I],
RA [auth E],
SB [auth J],
T [auth A],
WB [auth K],
XA [auth F]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
PG4
Query on PG4

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HA [auth D],
LA [auth D]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
AKG (Subject of Investigation/LOI)
Query on AKG

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AC [auth L]
BA [auth B]
EB [auth G]
GA [auth C]
HB [auth H]
AC [auth L],
BA [auth B],
EB [auth G],
GA [auth C],
HB [auth H],
LB [auth I],
NA [auth D],
QA [auth E],
RB [auth J],
U [auth A],
VB [auth K],
WA [auth F]
2-OXOGLUTARIC ACID
C5 H6 O5
KPGXRSRHYNQIFN-UHFFFAOYSA-N
PEG
Query on PEG

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AB [auth G]
BB [auth G]
CB [auth G]
JA [auth D]
KA [auth D]
AB [auth G],
BB [auth G],
CB [auth G],
JA [auth D],
KA [auth D],
N [auth A],
OB [auth J],
P [auth A],
TB [auth K],
ZA [auth G]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
S [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MOE
Query on MOE

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X [auth B],
YA [auth F]
METHOXY-ETHOXYL
C3 H7 O2
ASQUQUOEFDHYGP-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
CA [auth C]
DA [auth C]
DB [auth G]
EA [auth C]
GB [auth H]
CA [auth C],
DA [auth C],
DB [auth G],
EA [auth C],
GB [auth H],
IA [auth D],
JB [auth I],
KB [auth I],
M [auth A],
NB [auth I],
O [auth A],
OA [auth E],
PB [auth J],
Q [auth A],
QB [auth J],
R [auth A],
SA [auth F],
TA [auth F],
UA [auth F],
V [auth B],
VA [auth F],
W [auth B],
XB [auth L],
Y [auth B],
YB [auth L],
ZB [auth L]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
PA [auth E],
UB [auth K],
Z [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.183 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.337α = 60.04
b = 131.773β = 87.72
c = 131.507γ = 67.34
Software Package:
Software NamePurpose
BUSTERrefinement
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Max Planck SocietyGermanyna
German Research Foundation (DFG)GermanyKU 3768/1-1

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-24
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Database references