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Overview for MACiE Entry M0252

Version history

General Information

EC Number: 4.1.1.48 (A member of the Lyases, Carbon-carbon lyases, Carboxy-lyases)

Enzyme Name: indole-3-glycerol-phosphate synthase

Biological Species: Sulfolobus solfataricus (Archaea)

Catalytic Chain UniprotKB Accession Codes:

  • Q06121 - Indole-3-glycerol phosphate synthase

Representative PDB Code: 1igs - INDOLE-3-GLYCEROLPHOSPHATE SYNTHASE FROM SULFOLOBUS SOLFATARICUS AT2.0 A RESOLUTION (Resolution = 2.00 Å).

Catalytic CATH Codes:

Display structure information

Overall Reaction:

Image of proton

Image of 1-(2-Carboxyphenylamino)-1'-deoxy-D-ribulose 5'-phosphate

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Image of carbon dioxide

Image of Indoleglycerol phosphate

Image of water

proton
C00080
CHEBI:24636
1-(2-Carboxyphenylamino)-1'-deoxy-D-ribulose 5'-phosphate
C01302
CHEBI:58613
carbon dioxide
C00011
CHEBI:16526
Indoleglycerol phosphate
C03506
CHEBI:18299
water
C00001
CHEBI:15377

View similar reactions


Stepwise Description of the Reaction

Step 1The nitrogen in the substrate initiates a double bond rearrangement which results in the cyclisation of the intermediate, and deprotonation of Lys110.
Step 2The carboxylic acid group undergoes elimination from the substrate resulting indecarboxylation.
Step 3In this inferred step, Lys110 deprotonates water.
Step 4Glu159 deprotonates the carbon alpha to the nitrogen in the newly formed ring, initiating the elimination of water and the deprotonation of Lys110.
Step 5In this inferred return step, water deprotonates Glu159 and Lys110 deprotonates water.

View similar reactions (composite manual annotation)


Catalytic Residues Involved

Type Number Chain Location of Function
Lys 53 A Side Chain
Glu 51 A Side Chain
Lys 110 A Side Chain
Glu 159 A Side Chain
Asn 180 A Side Chain
Ser 211 A Side Chain

References

  1. M. Hennig et al. (2002), J. Mol. Biol., 319, 757-766. The catalytic mechanism of indole-3-glycerol phosphate synthase: crystal structures of complexes of the enzyme from Sulfolobus solfataricus with substrate analogue, substrate, and product.
    Medline: 12054868

Homologue information for M0252 (1igs)

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
0.14920.0145Compare
M0108 2,4-dienoyl-CoA reductase (NADPH)
1.3.1.34
1ps9 3.20.20.70
0.30.1384Compare
M0109 dihydroorotate oxidase
1.3.3.1
1d3g 3.20.20.70
0.31250.2548Compare
M0111 glutamate synthase (ferredoxin)
1.4.7.1
1ofd 3.20.20.70
0.45510.2920Compare
M0114 trimethylamine dehydrogenase
1.5.8.2
2tmd 3.20.20.70
0.32070Compare
M0319 NADPH dehydrogenase
1.6.99.1
1oya 3.20.20.70
0.2380.1199Compare
M0148 transaldolase
2.2.1.2
1onr 3.20.20.70
0.3870.3873Compare
M0008 nicotinate-nucleotide diphosphorylase (carboxylating)
2.4.2.19
1qpr 3.20.20.70
0.3750.3977Compare
M0243 pyridoxine 5'-phosphate synthase
2.6.99.2
1ho1 3.20.20.70
0.45740.1996Compare
M0050 orotidine-5'-phosphate decarboxylase
4.1.1.23
1dbt 3.20.20.70
0.19040.1529Compare
M0236 3-dehydro-L-gulonate-6-phosphate decarboxylase
4.1.1.85
1q6l 3.20.20.70
0.38090.36Compare
M0052 fructose-bisphosphate aldolase (Class II)
4.1.2.13
1b57 3.20.20.70
0.51850.2822Compare
M0222 fructose-bisphosphate aldolase (Class I)
4.1.2.13
2qut 3.20.20.70
0.32330.675Compare
M0054 3-dehydroquinate dehydratase (type I)
4.2.1.10
1qfe 3.20.20.70
0.31960.4157Compare
M0230 porphobilinogen synthase
4.2.1.24
1gzg 3.20.20.70
0.42850.36Compare
M0267 dihydrodipicolinate synthase
4.2.1.52
1dhp 3.20.20.70
0.440.1636Compare
M0270 ribulose-phosphate 3-epimerase
5.1.3.1
1h1z 3.20.20.70
0.38090.0642Compare
M0324 triosephosphate isomerase
5.3.1.1
1tph 3.20.20.70
0.44680.4999Compare
M0223 pyruvate carboxylase
6.4.1.1
2qf7 3.20.20.70
0.40470.1384Compare

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


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
Link to EzCatDB

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tryptophan biosynthetic process (biological process)
catalytic activity (molecular function)
indole-3-glycerol-phosphate synthase activity (molecular function)
tryptophan metabolic process (biological process)
metabolic process (biological process)
cellular amino acid biosynthetic process (biological process)
aromatic amino acid family biosynthetic process (biological process)
lyase activity (molecular function)
carboxy-lyase activity (molecular function)
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