2VDC

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


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history


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

  • DOI: 10.1074/jbc.M708529200
  • Structures With Same Primary Citation

  • 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, p ...

    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.


    Organizational Affiliation

    D├ępartement de Biologie Structurale, IMPMC-UMR 7590, CNRS, Universit├ęs Paris 6 et Paris 7, IPGP, Paris, France.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GLUTAMATE SYNTHASE [NADPH] LARGE CHAIN
A, B, C, D, E, F
1472Azospirillum brasilenseMutation(s): 0 
Gene Names: gltB
EC: 1.4.1.13
Find proteins for Q05755 (Azospirillum brasilense)
Go to UniProtKB:  Q05755
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
GLUTAMATE SYNTHASE [NADPH] SMALL CHAIN
G, H, I, J, K, L
456Azospirillum brasilenseMutation(s): 0 
Gene Names: gltD
EC: 1.4.1.13
Find proteins for Q05756 (Azospirillum brasilense)
Go to UniProtKB:  Q05756
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download CCD File 
G, H, I, J, K, L
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
FMN
Query on FMN

Download CCD File 
A, B, C, D, E, F
FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
SF4
Query on SF4

Download CCD File 
G, H, I, J, K, L
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
F3S
Query on F3S

Download CCD File 
A, B, C, D, E, F
FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-MZMDZPPWAW
 Ligand Interaction
OMT
Query on OMT

Download CCD File 
A, B, C, D, E, F
S-DIOXYMETHIONINE
C5 H11 N O4 S
UCUNFLYVYCGDHP-BYPYZUCNSA-N
 Ligand Interaction
AKG
Query on AKG

Download CCD File 
A, B, C, D, E, F
2-OXOGLUTARIC ACID
C5 H6 O5
KPGXRSRHYNQIFN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

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

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

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