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Overview for MACiE Entry M0304

Version history

General Information

EC Number: 1.4.1.13 (A member of the Oxidoreductases, Acting on the CH-NH2 group of donors, With NAD+ or NADP+ as acceptor)

Enzyme Name: glutamate synthase (NADPH)

Biological Species: Azospirillum brasilense (Bacteria)

Catalytic Chain UniprotKB Accession Codes:

  • Q05755 - Glutamate synthase [NADPH] large chain

Representative PDB Code: 1ea0 - ALPHA SUBUNIT OF A. BRASILENSE GLUTAMATE SYNTHASE (Resolution = 3.0 Å).

Catalytic CATH Codes:

  • 3.60.20.10 - Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1

"Other" CATH Codes:

Display structure information

Overall Reaction:

Image of NADPH

Image of L-glutamine

Image of proton

Image of 2-oxoglutarate

right arrow

Image of NADP

Image of L-glutamic acid

Image of L-glutamate

NADPH
C00005
CHEBI:16474
L-glutamine
C00064
CHEBI:58359
proton
C00080
CHEBI:24636
2-oxoglutarate
C00026
CHEBI:30916
NADP
C00006
CHEBI:18009
L-glutamic acid
C00025
CHEBI:16015
L-glutamate
C00025
CHEBI:29985

This reaction is irreversible.

Overall Comment: Glutamine hydrolysis is absent (or negligible) in the absence of the other substrates. The enzyme also catalyses the oxidation of NADPH, the ammonia-dependent synthesis of glutamate from 2-oxoglutarate and ammonia and the oxidation of L-glutamate in the presence of iodonitrotetrazolium salts, the latter two of which only occur at high pH. There is still much to be determined with respect to the mechanism of this enzyme [2] as well as how the cross-control of the synthase and glutaminase activities occurs with such precision. This enzyme utilises three iron-sulfur clusters (two Fe4S4 and one Fe3S4) as well as FMN and FAD as cofactors.


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Stepwise Description of the Reaction

Step 1NADP reduces the FAD cofactor.
Step 2A single electron is transferred from FAD, via the iron-sulfur clusters and Met479 to the FMN cofactor.
Step 3A second single electron is transferred from FAD, via the iron-sulfur clusters and Met479 to the FMN cofactor.
Step 4The N-terminus of Cys1 deprotonates water, which deprotonates the thiol group of Cys1, initiating a nucleophilic attack on the amide carbon in an addition reaction.
Step 5The oxyanion initiates an elimination that cleaves ammonia from the bound L-glutamine substrate. Ammonia deprotonates water, which deprotonates the N-terminus of Cys1.
Step 6The N-terminus of Cys1 deprotonates water, which initiates a nucleophilic attack on the carbonyl carbon of the covalently bound intermediate in an addition reaction.
Step 7The oxyanion initiates an elimination that cleaves the C-S bond, the thiolate of Cys1 deprotonates water, which deprotonates the N-terminus of Cys1.
Step 8Ammonia initiates a nucleophilic attack on the C2 of 2-oxoglutarate in an addition reaction.
Step 9Water is produced through an intramolecular elimination forming the 2-iminoglutarate intermediate.
Step 10FMN donates a hydride to the 2-iminoglutarate intermediate.

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Catalytic Residues Involved

Type Number Chain Location of Function
Cys 1 A Side Chain
Main Chain N Terminus
Asn 231 A Side Chain
Gly 230 A Main Chain Amide

Organic Cofactors for M0304

Type Identity Chain
FMN FMN 2974 A Overview
FAD FAD 0 Overview

Metal Cofactors for M0304

Type Het group Number Chain
iron SF4 483 G Overview
iron SF4 482 G Overview
iron F3S 2476 A Overview

References

  1. C. Binda et al. (2000), Structure, 8, 1299-1308. Cross-talk and ammonia channeling between active centers in the unexpected domain arrangement of glutamate synthase.
    Medline: 11188694
  2. M. A. Vanoni et al. (2008), IUBMB Life, 60, 287-300. Structure-function studies of glutamate synthases: a class of self-regulated iron-sulfur flavoenzymes essential for nitrogen assimilation.
    Medline: 18421771
  3. S. Ravasio et al. (2001), Biochemistry, 40, 5533-5541. Determination of the midpoint potential of the FAD and FMN flavin cofactors and of the 3Fe-4S cluster of glutamate synthase.
    Medline: 11331018
  4. R. H. van den Heuvel et al. (2003), J. Mol. Biol., 330, 113-128. The active conformation of glutamate synthase and its binding to ferredoxin.
    Medline: 12818206

Homologue information for M0304 (1ea0)

CSA Homologues

MACiE Homologues (within the PDB)

MACiE Homologues (within UniprotKB/SwissProt)



Entries with at least one Catalytic CATH code in common (different mechanisms):

MACiE Entry Enzyme Name
EC Number
PDB code CATH code Composite
Reaction Similarity
Catalytic Machinery
Similarity
M0111 glutamate synthase (ferredoxin)
1.4.7.1
1ofd 3.60.20.10
3.20.20.70
2.160.20.60
0.8530.2740Compare
M0214 amidophosphoribosyltransferase
2.4.2.14
1ecf 3.60.20.10
0.54870.6136Compare
M0082 glutamine-fructose-6-phosphate transaminase (isomerizing)
2.6.1.16
1jxa 3.60.20.10
0.78910.1927Compare
M0177 proteasome endopeptidase complex
3.4.25.1
1ryp 3.60.20.10
0.26260.0758Compare
M0302 asparagine synthase (glutamine-hydrolysing)
6.3.5.4
1ct9 3.60.20.10
0.5050.4686Compare

View a comparison of the other reactions in MACiE with the CATH domain 3.20.20.70

View a comparison of the other reactions in MACiE with the CATH domain 3.60.20.10


Links to this entry in other databases

Link to EC-PDB-SUM Link to PDB-SUM Link to RCSB PDB Link to PDBe Link to CSA
Link to MetaCyc Link to KEGG Link to BRENDA Link to ExplorENZ

GOA logo
catalytic activity (molecular function)
glutamate synthase (NADPH) activity (molecular function)
glutamate biosynthetic process (biological process)
glutamine metabolic process (biological process)
nitrogen compound metabolic process (biological process)
metabolic process (biological process)
cellular amino acid biosynthetic process (biological process)
glutamate synthase activity (molecular function)
oxidoreductase activity (molecular function)
oxidoreductase activity, acting on the CH-NH2 group of donors (molecular function)
metal ion binding (molecular function)
iron-sulfur cluster binding (molecular function)
3 iron, 4 sulfur cluster binding (molecular function)
oxidation-reduction process (biological process)
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