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Information on EC 4.1.2.8 - indole-3-glycerol-phosphate lyase
for references in articles please use BRENDA:EC4.1.2.8reinstated 2006, had been eliminated in 1972
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EC Tree
4.1.2.8 indole-3-glycerol-phosphate lyaseIUBMB Comments
Forms part of the defence mechanism against insects and microbial pathogens in the grass family, Gramineae, where it catalyses the first committed step in the formation of the cyclic hydroxamic acids 2,4-dihydroxy-2H-1,4-benzoxazin-3(4H)-one (DIBOA) and 2,4-dihydroxy-7-methoxy-2H-1,4-benzoxazin-3(4H)-one (DIMBOA) . This enzyme resembles the alpha-subunit of EC 4.2.1.20, tryptophan synthase , for which, (1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate is also a substrate, but, unlike tryptophan synthase, its activity is independent of the beta-subunit and free indole is released .
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Word Map
- 4.1.2.8
- pyridoxal
- l-serine
- l-tryptophan
-
aldimine
- alpha-aminoacrylate
-
alpha-glycerol
-
beta-replacement
- beta-chloro-l-alanine
-
benzoxazinoids
-
yanofsky
- diboa
-
ahmed
The expected taxonomic range for this enzyme is: Eukaryota, Bacteria
Reaction Schemes
Synonyms
tryptophan synthase alpha, tryptophan synthase alpha subunit, indole-3-glycerol phosphate lyase, indole synthase, zmtsa, os03g58300, indole-3-glycerol-phosphate lyase, 
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
BX1
IGL
indole synthase
tryptophan synthase alpha
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
(1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate = indole + D-glyceraldehyde 3-phosphate
-
-
-
-
(1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate = indole + D-glyceraldehyde 3-phosphate
the indole is further converted to 2,4-dihydroxy-7-methoxy-2H-1,4-benzoxazin-3(4H)-one, a secondary plant metabolite. BX1 cleaves indole-3-glycerol phosphate significantly faster to indole and glyceraldehyde 3-phosphate than the homologous alpha-subunit of tryptophan synthase, EC 4.2.1.20. In the primary metabolism, indole diffuses through the connecting tunnel to the beta-active site where it is condensed with serine to form tryptophan and water
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PATHWAY SOURCE
PATHWAYS
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SYSTEMATIC NAME
IUBMB Comments
(1S,2R)-1-C-(indol-3-yl)glycerol-3-phosphate D-glyceraldehyde-3-phosphate-lyase (indole-forming)
Forms part of the defence mechanism against insects and microbial pathogens in the grass family, Gramineae, where it catalyses the first committed step in the formation of the cyclic hydroxamic acids 2,4-dihydroxy-2H-1,4-benzoxazin-3(4H)-one (DIBOA) and 2,4-dihydroxy-7-methoxy-2H-1,4-benzoxazin-3(4H)-one (DIMBOA) [1]. This enzyme resembles the alpha-subunit of EC 4.2.1.20, tryptophan synthase [3], for which, (1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate is also a substrate, but, unlike tryptophan synthase, its activity is independent of the beta-subunit and free indole is released [2].
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CAS REGISTRY NUMBER
COMMENTARY
9014-52-2
-
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
additional information
?
-
-
indole release activated by beet armyworm and methyl salicylate is preceded by igl gene (encoding indole-3-glycerol phosphate lyase) induction within 1.5 h of treatment and declines within 6 h, induction of the IGL gene expression is not observed with (Z)-3-hexenol treatment
-
-
?
(1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate
indole + D-glyceraldehyde 3-phosphate
-
-
-
?
(1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate
indole + D-glyceraldehyde 3-phosphate
-
-
-
?
(1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate
indole + D-glyceraldehyde 3-phosphate
-
-
-
-
?
(1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate
indole + D-glyceraldehyde 3-phosphate
-
-
-
?
indole-3-glycerol phosphate
indole + D-glyceraldehyde 3-phosphate
-
-
-
-
?
indole-3-glycerol phosphate
indole + D-glyceraldehyde 3-phosphate
-
alpha-site cleaves the C3-C30 bond of IGP
-
-
?
indole-3-glycerol phosphate
indole + glyceraldehyde 3-phosphate
-
branch point from tryptophan biosynthesis, the enzyme is required for biosynthesis of 2,4-dihydroxy-7-methoxy-1,4-benzoxazin-3-one
-
-
?
indole-3-glycerol phosphate
indole + glyceraldehyde 3-phosphate
Igl transcript level is elevated by volicitin
-
-
?
indole-3-glycerol phosphate
indole + glyceraldehyde 3-phosphate
-
the indole-3-glycerol phosphate lyase Igl is the structural gene of volatile indole biosynthesis in the tritrophic interaction in maize. The gene is activated on transcriptional level with the same kinetics and to the same level by the fatty acid amino acid conjugates volicitin and N-linolenoyl-L-glutamine. Both conjugates are present in the regurgitates of herbivorous caterpillars. Modifications of the fatty acid moiety of the fatty acid amino acid conjugates greatly reduces the elicitation of Igl and only the L-stereoisomer of the fatty acid amino acid conjugates shows biological activity in the system. Volicitin treatment leads to a fast increase of allene oxide synthase and allene oxide cyclase transcription levels and methyl jasmonate application induces Igl transcription. Hence,the induction of jasmonate biosynthesis appears to be an integral part of the elicitor mediated increase of Igl gene transcription
-
-
?
indole-3-glycerol phosphate
indole + glyceraldehyde 3-phosphate
the indole is further converted to 2,4-dihydroxy-7-methoxy-2H-1,4-benzoxazin-3(4H)-one, a secondary plant metabolite. BX1 cleaves indole-3-glycerol phosphate significantly faster to indole and glyceraldehyde 3-phosphate than the homologous alpha-subunit of tryptophan synthase, EC 4.2.1.20
-
-
?
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NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
additional information
?
-
-
indole release activated by beet armyworm and methyl salicylate is preceded by igl gene (encoding indole-3-glycerol phosphate lyase) induction within 1.5 h of treatment and declines within 6 h, induction of the IGL gene expression is not observed with (Z)-3-hexenol treatment
-
-
?
(1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate
indole + D-glyceraldehyde 3-phosphate
-
-
-
?
(1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate
indole + D-glyceraldehyde 3-phosphate
-
-
-
-
?
(1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate
indole + D-glyceraldehyde 3-phosphate
-
-
-
?
indole-3-glycerol phosphate
indole + glyceraldehyde 3-phosphate
-
branch point from tryptophan biosynthesis, the enzyme is required for biosynthesis of 2,4-dihydroxy-7-methoxy-1,4-benzoxazin-3-one
-
-
?
indole-3-glycerol phosphate
indole + glyceraldehyde 3-phosphate
Igl transcript level is elevated by volicitin
-
-
?
indole-3-glycerol phosphate
indole + glyceraldehyde 3-phosphate
-
the indole-3-glycerol phosphate lyase Igl is the structural gene of volatile indole biosynthesis in the tritrophic interaction in maize. The gene is activated on transcriptional level with the same kinetics and to the same level by the fatty acid amino acid conjugates volicitin and N-linolenoyl-L-glutamine. Both conjugates are present in the regurgitates of herbivorous caterpillars. Modifications of the fatty acid moiety of the fatty acid amino acid conjugates greatly reduces the elicitation of Igl and only the L-stereoisomer of the fatty acid amino acid conjugates shows biological activity in the system. Volicitin treatment leads to a fast increase of allene oxide synthase and allene oxide cyclase transcription levels and methyl jasmonate application induces Igl transcription. Hence,the induction of jasmonate biosynthesis appears to be an integral part of the elicitor mediated increase of Igl gene transcription
-
-
?
indole-3-glycerol phosphate
indole + glyceraldehyde 3-phosphate
the indole is further converted to 2,4-dihydroxy-7-methoxy-2H-1,4-benzoxazin-3(4H)-one, a secondary plant metabolite. BX1 cleaves indole-3-glycerol phosphate significantly faster to indole and glyceraldehyde 3-phosphate than the homologous alpha-subunit of tryptophan synthase, EC 4.2.1.20
-
-
?
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INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
2,3-dihydroxy-3-[(2-hydroxyphenyl)amino] propyl phosphate
-
competetive inhibitor
2-([[4-(trifluoromethoxy)phenyl]sulfonyl]amino) ethyl phosphate
-
competetive inhibitor
3-(1H-indol-3-yl)propyl phosphate
-
competetive inhibitor
3-(2,3-dihydro-1H-indol-3-yl)glycerol phosphate
-
competetive inhibitor
3-acetyl-L-aspartic acid
-
inhibits the alpha-reaction. Indole 3-acetylglycine and 3-acetyl-L-aspartic acid are similar to complexes that are similar to 3-(1H-indol-3-yl)propyl phosphate with the phosphoryl sub-site occupied by the ligand carboxylate, the indole ring NH H-bonded to alphaAsp60, and one carboxylate oxygen of the catalytic alphaGlu49 H-bonded to the acetyl oxygen
-
4-[(2-aminophenyl)sulfonyl]butyl phosphate
-
competetive inhibitor
indole 3-acetylglycine
-
inhibits the alpha-reaction. Indole 3-acetylglycine and 3-acetyl-L-aspartic acid are similar to complexes that are similar to 3-(1H-indol-3-yl)propyl phosphate with the phosphoryl sub-site occupied by the ligand carboxylate, the indole ring NH H-bonded to alphaAsp60, and one carboxylate oxygen of the catalytic alphaGlu49 H-bonded to the acetyl oxygen
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ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
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SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
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LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
physiological function
-
in an isoform Igl deficient background, mutant plants deficient in chloroplastic isoform Bx1 allow better development of the cereal aphid Rhopalosiphum padi, and are affected in penetration resistance against the fungus Setosphaeria turtica. At stages preceding major tissue disruption, Rhopalosiphum padi and Setosphaeria turtica elicited increased accumulation of 2,4-dihydroxy-7-methoxy-2H-1,4-benzoxazin-3(4H)-one-glucoside, 2,4-dihydroxy-7-methoxy-2H-1,4-benzoxazin-3(4H)-one, and 2-hydroxy-4,7-dimethoxy-1,4-benzoxazin-3-one-glucoside (HDMBOA-glc), which is most pronounced in apoplastic leaf extracts. Chloroplastic isoform-deficient bx1 mutant lines deposite less chitosan-induced callose than Bx1 wild-type lines, whereas apoplast infiltration with 2,4-dihydroxy-7-methoxy-2H-1,4-benzoxazin-3(4H)-one, but not HDMBOA-glc, mimicks chitosan-induced callose
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UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable).
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable). TRPA1_ARATH
275
0
29579
Swiss-Prot
other Location (Reliability: 3)
TRPA2_ARATH
312
0
33200
Swiss-Prot
Chloroplast (Reliability: 3)
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SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
the crystal structure of tryptophan synthase is determined at 2.1 A resolution
-
the crystal structure of BX1 suggusts that the faster catalytic rate of BX1 compared to the homologous alpha-subuni8t of tryptophan synthase EC 4.2.1.20, may due to a stabilzation of the active conformation, loop alphaL6 is closed and the catalytic glutamate, Glu134 is in the active conformation. There are two crystallographically independent molecules in the asymmetric unit of the rhombohedral BX1 crystal form
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
up
PtINS has about two to fivefolds higher transcript level than that of PtTSA (tryptophan synthase alpha-subunit). After treatment with 2,1,3-benzothiadiazole the relative transcript level of PtINS (indole synthase) over PtTSA (tryptophan synthase alpha-subunit) is significantly enhanced in the plant
D60N
-
site-directed mutagenesis, substitution of asparagine for aspartic acid in the alphaAsp60Asn variant. alphaAsp60 has an essential role in stabilizing charge development on the IGP indole ring during C-C bond scission
Q114N
-
betaGln114Asn mutation, which shortens the betaGln114 side chain connecting the betaL3 loop with the rest of the protein, resulted in two fractions of enzyme
T183V
-
site-directed mutagenesis, substitution of valine for threonine in the alphaThr183Val variant, resulting in impaired catalysis at the alpha-site and loss of allosteric communication
Y110V
-
betaThr110Val mutation, which replaces a hydrogen bonding partner to the substrate carboxylate with a methyl group severely decreased the ability to form the aminoacrylate external aldimine E(AA) and consequently severely impaired beta-reaction and alphabeta-reaction
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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant protein by His-tag affinity purification via Ni-NTA agarose, plant protein by anion exchange and gel permeation chromatography
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
CaMV35S-INS-GFP and CaMV35-TSA1-GFP are constructed, the INS open reading frame is subcloned into the vector pQE81
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EXPRESSION
ORGANISM
UNIPROT
LITERATURE
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Kulik, V.; Hartmann, E.; Weyand, M.; Frey, M.; Gierl, A.; Niks, D.; Dunn, M.F.; Schlichting, I.
On the structural basis of the catalytic mechanism and the regulation of the alpha subunit of tryptophan synthase from Salmonella typhimurium and BX1 from maize, two evolutionarily related enzymes
J. Mol. Biol.
352
608-620
2005
Zea mays (P42390)
brenda
Yanofsky, C.
The enzymatic conversion of anthranilic acid to indole
J. Biol. Chem.
223
171-184
1956
Escherichia coli
brenda
Frey, M.; Spiteller, D.; Boland, W.; Gierl, A.
Transcriptional activation of Igl, the gene for indole formation in Zea mays: a structure-activity study with elicitor-active N-acyl glutamines from insects
Phytochemistry
65
1047-1055
2004
Zea mays
brenda
Farag, M.A.; Fokar, M.; Abd, H.; Zhang, H.; Allen, R.D.; Pare, P.W.
(Z)-3-Hexenol induces defense genes and downstream metabolites in maize
Planta
220
900-909
2005
Zea mays
brenda
Melanson, D.; Chilton, M.D.; Masters-Moore, D.; Chilton, W.S.
A deletion in an indole synthase gene is responsible for the DIMBOA-deficient phenotype of bxbx maize
Proc. Natl. Acad. Sci. USA
94
13345-13350
1997
Zea mays (P42390), Zea mays
brenda
Frey, M.; Stettner, C.; Pare, P.W.; Schmelz, E.A.; Tumlinson, J.H.; Gierl, A.
An herbivore elicitor activates the gene for indole emission in maize
Proc. Natl. Acad. Sci. USA
97
14801-14806
2000
Zea mays (Q9FQ77), Zea mays
brenda
Frey, M.; Chomet, P.; Glawischnig, E.; Stettner, C.; Grun, S.; Winklmair, A.; Eisenreich, W.; Bacher, A.; Meeley, R.B.; Briggs, S.P.; Simcox, K.; Gierl, A.
Analysis of a chemical plant defense mechanism in grasses
Science
277
696-699
1997
Zea mays
brenda
Kriechbaumer, V.; Weigang, L.; Fiesselmann, A.; Letzel, T.; Frey, M.; Gierl, A.; Glawischnig, E.
Characterisation of the tryptophan synthase alpha subunit in maize
BMC Plant Biol.
8
44
2008
Zea mays (B2Y0K4), Zea mays
brenda
Barends, T.R.; Domratcheva, T.; Kulik, V.; Blumenstein, L.; Niks, D.; Dunn, M.F.; Schlichting, I.
Structure and mechanistic implications of a tryptophan synthase quinonoid intermediate
ChemBioChem
9
1024-1028
2008
Salmonella enterica subsp. enterica serovar Typhimurium
brenda
Barends, T.R.; Dunn, M.F.; Schlichting, I.
Tryptophan synthase, an allosteric molecular factory
Curr. Opin. Chem. Biol.
12
593-600
2008
Salmonella enterica subsp. enterica serovar Typhimurium
brenda
Zhang, R.; Wang, B.; Ouyang, J.; Li, J.; Wang, Y.
Arabidopsis indole synthase, a homolog of tryptophan synthase alpha, is an enzyme involved in the Trp-independent indole-containing metabolite biosynthesis
J. Integr. Plant Biol.
50
1070-1077
2008
Arabidopsis thaliana (O22765)
brenda
Dunn, M.F.; Niks, D.; Ngo, H.; Barends, T.R.; Schlichting, I.
Tryptophan synthase: the workings of a channeling nanomachine
Trends Biochem. Sci.
33
254-264
2008
Salmonella enterica subsp. enterica serovar Typhimurium
brenda
Zhuang, X.; Fiesselmann, A.; Zhao, N.; Chen, H.; Frey, M.; Chen, F.
Biosynthesis and emission of insect herbivory-induced volatile indole in rice
Phytochemistry
73
15-22
2012
Oryza sativa (Q7Y1I9), Oryza sativa
brenda
Ahmad, S.; Veyrat, N.; Gordon-Weeks, R.; Zhang, Y.; Martin, J.; Smart, L.; Glauser, G.; Erb, M.; Flors, V.; Frey, M.; Ton, J.
Benzoxazinoid metabolites regulate innate immunity against aphids and fungi in maize
Plant Physiol.
157
317-327
2011
Zea mays
brenda
Jin, Z.; Kim, J.H.; Park, S.U.; Kim, S.U.
Cloning and characterization of indole synthase (INS) and a putative tryptophan synthase alpha-subunit (TSA) genes from Polygonum tinctorium
Plant Cell Rep.
35
2449-2459
2016
Persicaria tinctoria (A0A1C9CXC5), Persicaria tinctoria
brenda
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Release 2023.1 (January 2023)
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