2VDC

THE 9.5 A RESOLUTION STRUCTURE OF GLUTAMATE SYNTHASE FROM CRYO-ELECTRON MICROSCOPY AND ITS OLIGOMERIZATION BEHAVIOR IN SOLUTION: FUNCTIONAL IMPLICATIONS.

• PDB DOI:  https://doi.org/10.2210/pdb2VDC/pdb
• EM Map EMD-1440: EMDB EMDataResource

• Classification: OXIDOREDUCTASE
• Organism(s): Azospirillum brasilense
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-10-04 Released: 2008-01-15 
• Deposition Author(s): Cottevieille, M., Larquet, E., Jonic, S., Petoukhov, M.V., Caprini, G., Paravisi, S., Svergun, D.I., Vanoni, M.A., Boisset, N.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 9.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

The Subnanometer Resolution Structure of the Glutamate Synthase 1.2-Mda Hexamer by Cryoelectron Microscopy and its Oligomerization Behavior in Solution: Functional Implications.

Cottevieille, M., Larquet, E., Jonic, S., Petoukhov, M.V., Caprini, G., Paravisi, S., Svergun, D.I., Vanoni, M.A., Boisset, N.

(2008) J Biol Chem 283: 8237-8249

• PubMed: 18199747 
• DOI: https://doi.org/10.1074/jbc.M708529200
• Primary Citation of Related Structures:  
  2VDC


• PubMed Abstract: 
  

The three-dimensional structure of the hexameric (alphabeta)(6) 1.2-MDa complex formed by glutamate synthase has been determined at subnanometric resolution by combining cryoelectron microscopy, small angle x-ray scattering, and molecular modeling, providing for the first time a molecular model of this complex iron-sulfur flavoprotein. In the hexameric species, interprotomeric alpha-alpha and alpha-beta contacts are mediated by the C-terminal domain of the alpha subunit, which is based on a beta helical fold so far unique to glutamate synthases. The alphabeta protomer extracted from the hexameric model is fully consistent with it being the minimal catalytically active form of the enzyme. The structure clarifies the electron transfer pathway from the FAD cofactor on the beta subunit, to the FMN on the alpha subunit, through the low potential [4Fe-4S](1+/2+) centers on the beta subunit and the [3Fe-4S](0/1+) cluster on the alpha subunit. The (alphabeta)(6) hexamer exhibits a concentration-dependent equilibrium with alphabeta monomers and (alphabeta)(2) dimers, in solution, the hexamer being destabilized by high ionic strength and, to a lower extent, by the reaction product NADP(+). Hexamerization seems to decrease the catalytic efficiency of the alphabeta protomer only 3-fold by increasing the K(m) values measured for l-Gln and 2-OG. However, it cannot be ruled out that the (alphabeta)(6) hexamer acts as a scaffold for the assembly of multienzymatic complexes of nitrogen metabolism or that it provides a means to regulate the activity of the enzyme through an as yet unknown ligand.

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Organizational Affiliation: 

Département de Biologie Structurale, IMPMC-UMR 7590, CNRS, Universités Paris 6 et Paris 7, IPGP, Paris, France.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (3D View)
Global Stoichiometry: Hetero 12-mer - A6B6 

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

Macromolecule Content

• Total Structure Weight: 1,281.31 kDa 
• Atom Count: 89,598 
• Modelled Residue Count: 11,568 
• Deposited Residue Count: 11,568 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GLUTAMATE SYNTHASE [NADPH] LARGE CHAIN	A, B, C, D, E, F	1,472	Azospirillum brasilense	Mutation(s): 0  Gene Names: gltB EC: 1.4.1.13
UniProt
Find proteins for Q05755 (Azospirillum brasilense) Explore Q05755  Go to UniProtKB:  Q05755

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
GLUTAMATE SYNTHASE [NADPH] SMALL CHAIN	G, H, I, J, K, L	456	Azospirillum brasilense	Mutation(s): 0  Gene Names: gltD EC: 1.4.1.13
UniProt
Find proteins for Q05756 (Azospirillum brasilense) Explore Q05756  Go to UniProtKB:  Q05756

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	BB [auth L], MA [auth G], PA [auth H], SA [auth I], VA [auth J], YA [auth K]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
FMN	DA [auth E], HA [auth F], N [auth A], R [auth B], V [auth C], Z [auth D]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
SF4	AB [auth L], KA [auth G], LA [auth G], NA [auth H], OA [auth H], QA [auth I], RA [auth I], TA [auth J], UA [auth J], WA [auth K], XA [auth K], ZA [auth L]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-VKOJMFJBAC
F3S	BA [auth D], FA [auth E], JA [auth F], P [auth A], T [auth B], X [auth C]	FE3-S4 CLUSTER Fe3 S4 FCXHZBQOKRZXKS-MZMDZPPWAW
OMT	CA [auth E], GA [auth F], M [auth A], Q [auth B], U [auth C], Y [auth D]	S-DIOXYMETHIONINE C5 H11 N O4 S UCUNFLYVYCGDHP-BYPYZUCNSA-N
AKG	AA [auth D], EA [auth E], IA [auth F], O [auth A], S [auth B], W [auth C]	2-OXOGLUTARIC ACID C5 H6 O5 KPGXRSRHYNQIFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 9.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	SPIDER

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-01-15 
Deposition Author(s): Cottevieille, M., Larquet, E., Jonic, S., Petoukhov, M.V., Caprini, G., Paravisi, S., Svergun, D.I., Vanoni, M.A., Boisset, N.

Revision History  

• Version 1.0: 2008-01-15
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-08-23
  Changes: Data collection
• Version 1.4: 2019-10-23
  Changes: Data collection, Other
• Version 1.5: 2019-11-20
  Changes: Advisory, Derived calculations