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23  structures 3907  species 3  interactions 5164  sequences 18  architectures

Family: IGPS (PF00218)

Summary: Indole-3-glycerol phosphate synthase

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This is the Wikipedia entry entitled "Indole-3-glycerol-phosphate synthase". More...

Indole-3-glycerol-phosphate synthase Edit Wikipedia article

indole-3-glycerol-phosphate synthase
Identifiers
EC number 4.1.1.48
CAS number 9031-60-1
Databases
IntEnz IntEnz view
BRENDA BRENDA entry
ExPASy NiceZyme view
KEGG KEGG entry
MetaCyc metabolic pathway
PRIAM profile
PDB structures RCSB PDB PDBe PDBsum
Gene Ontology AmiGO / EGO
Indole-3-glycerol phosphate synthase
PDB 1pii EBI.jpg
three-dimensional structure of the bifunctional enzyme phosphoribosylanthranilate isomerase: indoleglycerolphosphate synthase from escherichia coli refined at 2.0 angstroms resolution
Identifiers
Symbol IGPS
Pfam PF00218
Pfam clan CL0036
InterPro IPR013798
PROSITE PDOC00536
SCOP 1pii
SUPERFAMILY 1pii

In enzymology, an indole-3-glycerol-phosphate synthase (IGPS) (EC 4.1.1.48) is an enzyme that catalyzes the chemical reaction

1-(2-carboxyphenylamino)-1-deoxy-D-ribulose 5-phosphate \rightleftharpoons 1-C-(indol-3-yl)-glycerol 3-phosphate + CO2 + H2O

Hence, this enzyme has one substrate, 1-(2-carboxyphenylamino)-1-deoxy-D-ribulose 5-phosphate, but 3 products: 1-C-(indol-3-yl)-glycerol 3-phosphate, CO2, and H2O.

This enzyme belongs to the family of lyases, to be specific, the carboxy-lyases, which cleave carbon-carbon bonds. The systematic name of this enzyme class is 1-(2-carboxyphenylamino)-1-deoxy-D-ribulose-5-phosphate carboxy-lyase [cyclizing 1-C-(indol-3-yl)glycerol-3-phosphate-forming]. Other names in common use include indoleglycerol phosphate synthetase, indoleglycerol phosphate synthase, indole-3-glycerophosphate synthase, 1-(2-carboxyphenylamino)-1-deoxy-D-ribulose-5-phosphate, and carboxy-lyase (cyclizing). This enzyme participates in phenylalanine, tyrosine and tryptophan biosynthesis and two-component system - general. It employs one cofactor, pyruvate.

Structural studies

In some bacteria, IGPS is a single chain enzyme. In others, such as Escherichia coli, it is the N-terminal domain of a bifunctional enzyme that also catalyses N-(5'-phosphoribosyl)anthranilate isomerase (EC 5.3.1.24) (PRAI) activity, the third step of tryptophan biosynthesis. In fungi, IGPS is the central domain of a trifunctional enzyme that contains a PRAI C-terminal domain and a glutamine amidotransferase (EC 2.4.2.-) (GATase) N-terminal domain.

A structure of the IGPS domain of the bifunctional enzyme from the mesophilic bacterium E. coli (eIGPS) has been compared with the monomeric indole-3-glycerol phosphate synthase from the hyperthermophilic archaeon Sulfolobus solfataricus (sIGPS). Both are single-domain (beta/alpha)8 barrel proteins, with one (eIGPS) or two (sIGPS) additional helices inserted before the first beta strand.[1]

As of late 2007, 11 structures have been solved for this class of enzymes, with PDB accession codes 1A53, 1I4N, 1J5T, 1JCM, 1JUK, 1JUL, 1LBF, 1LBL, 1PII, 1VC4, and 2C3Z.

References

  1. ^ Goldman A (December 1995). "How to make my blood boil". Structure 3 (12): 1277–9. doi:10.1016/s0969-2126(01)00263-5. PMID 8747452. 

Further reading

  • Creighton TE, Yanofsky C (1966). "Indole-3-glycerol phosphate synthetase of Escherichia coli, an enzyme of the tryptophan operon". J. Biol. Chem. 241 (20): 4616–24. PMID 5332729. 
  • Creighton TE and Yanofsky C (1970). "Chorismate to tryptophan (Escherichia coli) - Anthranilate synthetase, PR transferase, PRA isomerase, InGP synthetase, tryptophan synthetase". Methods Enzymol. 17A: 365–380. doi:10.1016/0076-6879(71)17215-1. 
  • Kung CC, Huang WN, Huang YC, Yeh KC (2006). "Proteomic survey of copper-binding proteins in Arabidopsis roots by immobilized metal affinity chromatography and mass spectrometry". Proteomics. 6 (9): 2746–58. doi:10.1002/pmic.200500108. PMID 16526091. 

This article incorporates text from the public domain Pfam and InterPro IPR013798


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External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR013798

Indole-3-glycerol phosphate synthase (EC) (IGPS) catalyses the fourth step in the biosynthesis of tryptophan, the ring closure of 1-(2-carboxy-phenylamino)-1-deoxyribulose into indol-3-glycerol-phosphate. In some bacteria, IGPS is a single chain enzyme. In others, such as Escherichia coli, it is the N-terminal domain of a bifunctional enzyme that also catalyses N-(5'-phosphoribosyl)anthranilate isomerase (EC) (PRAI) activity (see INTERPRO), the third step of tryptophan biosynthesis. In fungi, IGPS is the central domain of a trifunctional enzyme that contains a PRAI C-terminal domain and a glutamine amidotransferase (EC) (GATase) N-terminal domain (see INTERPRO).

A structure of the IGPS domain of the bifunctional enzyme from the mesophilic bacterium E. coli (eIGPS) has been compared with the monomeric indole-3-glycerol phosphate synthase from the hyperthermophilic archaeon Sulfolobus solfataricus (sIGPS). Both are single-domain (beta/alpha)8 barrel proteins, with one (eIGPS) or two (sIGPS) additional helices inserted before the first beta strand [PUBMED:8747452].

Gene Ontology

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Domain organisation

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Alignments

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  Seed
(20)
Full
(5164)
Representative proteomes NCBI
(4373)
Meta
(2572)
RP15
(350)
RP35
(707)
RP55
(929)
RP75
(1085)
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  Seed
(20)
Full
(5164)
Representative proteomes NCBI
(4373)
Meta
(2572)
RP15
(350)
RP35
(707)
RP55
(929)
RP75
(1085)
Alignment:
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  Seed
(20)
Full
(5164)
Representative proteomes NCBI
(4373)
Meta
(2572)
RP15
(350)
RP35
(707)
RP55
(929)
RP75
(1085)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

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Curation and family details

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Seed source: Prosite
Previous IDs: none
Type: Domain
Author: Finn RD
Number in seed: 20
Number in full: 5164
Average length of the domain: 228.50 aa
Average identity of full alignment: 40 %
Average coverage of the sequence by the domain: 76.40 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.0 20.0
Trusted cut-off 20.0 20.0
Noise cut-off 19.9 19.9
Model length: 254
Family (HMM) version: 16
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Species distribution

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Interactions

There are 3 interactions for this family. More...

PRAI SOR_SNZ IGPS

Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the IGPS domain has been found. There are 23 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.

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