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Overview for MACiE Entry M0111

Version history

General Information

EC Number: 1.4.7.1 (A member of the Oxidoreductases, Acting on the CH-NH2 group of donors, With an iron-sulfur protein as acceptor)

Enzyme Name: glutamate synthase (ferredoxin)

Biological Species: Synechocystis sp. (Bacteria)

Catalytic Chain UniprotKB Accession Codes:

  • P55038 - Ferredoxin-dependent glutamate synthase 2

Representative PDB Code: 1ofd - GLUTAMATE SYNTHASE FROM SYNECHOCYSTIS SP IN COMPLEX WITH2-OXOGLUTARATE AT 2.0 ANGSTROM RESOLUTION (Resolution = 2.00 Å).

Catalytic CATH Codes:

  • 3.60.20.10 - Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
  • 3.20.20.70 - Aldolase class I

"Other" CATH Codes:

Display structure information

Overall Reaction:

Image of L-glutamine

Image of proton

Image of reduced ferredoxin

Image of 2-oxoglutarate

right arrow

Image of oxidised ferredoxin

Image of L-glutamate

L-glutamine
C00064
CHEBI:58359
2 proton
C00080
CHEBI:24636
2 reduced ferredoxin
C00138
CHEBI:17513
2-oxoglutarate
C00026
CHEBI:16810
2 oxidised ferredoxin
C00139
CHEBI:17908
2 L-glutamate
C00025
CHEBI:29985

Overall Comment: This reaction occurs in two different domains within the same enzyme. The first four steps are catalysed in the amidotransferase domain (CATH code 3.60.20.10, residues 1-422). The following steps occur in the FMN-binding domain (CATH code 3.20.20.70, residues 787-1223). The two domains are bridged by an ammonia transfer tunnel, which provides a micro-environment that prevents the protonation of the ammonia, crucial as the enzyme will not function with ammonium as the nitrogen source.


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Stepwise Description of the Reaction

Step 1The N-terminus of Cys1 deprotonates deprotonates water, which deprotonates the thiol group of Cys1, initiating a nucleophilic attack on the amide carbon in an addition reaction.
Step 2The oxyanion initiates an elimination that cleaves ammonia from the bound L-glutamine substrate. Ammonia deprotonates water, which deprotonates the N-terminus of Cys1.
Step 3The N-terminus of Cys1 deprotonates water, which deprotonates another water that initiates a nucleophilic attack on the carbonyl carbon of the covalently bound intermediate in an addition reaction.
Step 4The oxyanion initiates an elimination that cleaves the C-S bond, the thiolate of Cys1 deprotonates water, which deprotonates the N-terminus of Cys1
Step 5Ammonia initiates a nucleophilic attack on the C2 carbonyl carbon of the 2-oxoglutarate substrate in an addition reaction. The oxyanion formed deprotonates the bound ammonium.
Step 6The amine initiates an elimination of the bound hydroxide as water, which deprotonates Lys972.
Step 7FMN eliminates a hydride ion, which adds to the C2 imine carbon in an addition reaction.
Step 8Lys972 deprotonates water in an inferred step.
Step 9Ferredoxin donates a single electron, which is transferred to FMN through an iron-sulfur cluster. FMN deprotonates water.
Step 10A second ferredoxin donates a single electron, which is transferred to FMN through an iron-sulfur cluster, which regenerates the reduced form of FMN.

View similar reactions (composite manual annotation)


Catalytic Residues Involved

Type Number Chain Location of Function
Cys 1 A Main Chain N Terminus
Side Chain
Arg 31 A Main Chain Carbonyl
Phe 207 A Main Chain Amide
Asn 227 A Side Chain
Gly 228 A Main Chain Amide
Glu 903 A Side Chain
Gln 969 A Side Chain
Lys 972 A Side Chain
Gln 978 A Main Chain Amide

Organic Cofactors for M0111

Type Identity Chain
FMN FMN 2508 A Overview

Metal Cofactors for M0111

Type Het group Number Chain
iron F3S 2509 A Overview

References

  1. 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
  2. R. H. H. van den Heuvel et al. (2004), Cell. Mol. Life Sci., 61, 669-681. Glutamate synthase: a fascinating pathway from L-glutamine to L-glutamate.
    Medline: 15052410
  3. C. Oinonen et al. (2000), Protein Sci., 9, 2329-2337. Structural comparison of Ntn-hydrolases.
    Medline: 11206054
  4. R. H. H. van den Heuvel et al. (2002), J. Biol. Chem., 277, 24579-24583. Structural studies on the synchronization of catalytic centers in glutamate synthase.
    Medline: 11967268

Homologue information for M0111 (1ofd)

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
M0102 L-lactate dehydrogenase (cytochrome)
1.1.2.3
1fcb 3.20.20.70
0.27380Compare
M0108 2,4-dienoyl-CoA reductase (NADPH)
1.3.1.34
1ps9 3.20.20.70
0.46070.2999Compare
M0109 dihydroorotate oxidase
1.3.3.1
1d3g 3.20.20.70
0.33540.1496Compare
M0304 glutamate synthase (NADPH)
1.4.1.13
1ea0 3.60.20.10
3.20.20.70
2.160.20.60
0.8530.2740Compare
M0114 trimethylamine dehydrogenase
1.5.8.2
2tmd 3.20.20.70
0.28660.0692Compare
M0319 NADPH dehydrogenase
1.6.99.1
1oya 3.20.20.70
0.26410.1205Compare
M0148 transaldolase
2.2.1.2
1onr 3.20.20.70
0.63850.1384Compare
M0214 amidophosphoribosyltransferase
2.4.2.14
1ecf 3.60.20.10
0.750.2571Compare
M0008 nicotinate-nucleotide diphosphorylase (carboxylating)
2.4.2.19
1qpr 3.20.20.70
0.21930.225Compare
M0082 glutamine-fructose-6-phosphate transaminase (isomerizing)
2.6.1.16
1jxa 3.60.20.10
0.8080.4331Compare
M0243 pyridoxine 5'-phosphate synthase
2.6.99.2
1ho1 3.20.20.70
0.6680.188Compare
M0177 proteasome endopeptidase complex
3.4.25.1
1ryp 3.60.20.10
0.34020.146Compare
M0050 orotidine-5'-phosphate decarboxylase
4.1.1.23
1dbt 3.20.20.70
0.06790.0599Compare
M0252 indole-3-glycerol-phosphate synthase
4.1.1.48
1igs 3.20.20.70
0.45510.2920Compare
M0236 3-dehydro-L-gulonate-6-phosphate decarboxylase
4.1.1.85
1q6l 3.20.20.70
0.23120.1384Compare
M0052 fructose-bisphosphate aldolase (Class II)
4.1.2.13
1b57 3.20.20.70
0.35760.1579Compare
M0222 fructose-bisphosphate aldolase (Class I)
4.1.2.13
2qut 3.20.20.70
0.57380.2133Compare
M0054 3-dehydroquinate dehydratase (type I)
4.2.1.10
1qfe 3.20.20.70
0.75190.1616Compare
M0230 porphobilinogen synthase
4.2.1.24
1gzg 3.20.20.70
0.74090.1491Compare
M0267 dihydrodipicolinate synthase
4.2.1.52
1dhp 3.20.20.70
0.58210.0785Compare
M0270 ribulose-phosphate 3-epimerase
5.1.3.1
1h1z 3.20.20.70
0.19860.0124Compare
M0324 triosephosphate isomerase
5.3.1.1
1tph 3.20.20.70
0.24830.1384Compare
M0302 asparagine synthase (glutamine-hydrolysing)
6.3.5.4
1ct9 3.60.20.10
0.67360.2935Compare
M0223 pyruvate carboxylase
6.4.1.1
2qf7 3.20.20.70
0.5350.0599Compare

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

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catalytic activity (molecular function)
protein binding (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)
glutamate synthase (ferredoxin) 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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