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24  structures 3613  species 1  interaction 3695  sequences 12  architectures

Family: IGPD (PF00475)

Summary: Imidazoleglycerol-phosphate dehydratase

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This is the Wikipedia entry entitled "Imidazoleglycerol-phosphate dehydratase". More...

Imidazoleglycerol-phosphate dehydratase Edit Wikipedia article

imidazoleglycerol-phosphate dehydratase
Identifiers
EC number 4.2.1.19
CAS number 9024-35-5
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
Imidazoleglycerol-phosphate dehydratase
PDB 1rhy EBI.jpg
crystal structure of imidazole glycerol phosphate dehydratase
Identifiers
Symbol IGPD
Pfam PF00475
Pfam clan CL0329
InterPro IPR000807
PROSITE PDOC00738
SCOP 1rhy
SUPERFAMILY 1rhy

In enzymology, an imidazoleglycerol-phosphate dehydratase (EC 4.2.1.19) is an enzyme that catalyzes the chemical reaction

D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate \rightleftharpoons 3-(imidazol-4-yl)-2-oxopropyl phosphate + H2O

Hence, this enzyme has one substrate, D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate, and two products, 3-(imidazol-4-yl)-2-oxopropyl phosphate and H2O. This reaction is the seventh step in the biosynthesis of histidine in bacteria, fungi and plants.

This enzyme belongs to the family of lyases, specifically the hydro-lyases, which cleave carbon-oxygen bonds. The systematic name of this enzyme class is D-erythro-1-(imidazol-4-yl)glycerol-3-phosphate hydro-lyase [3-(imidazol-4-yl)-2-oxopropyl-phosphate-forming]. Other names in common use include IGP dehydratase, and D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate hydro-lyase. This enzyme participates in histidine metabolism as it is involved in the 6th step of histidine biosynthesis as part of a nine step cyclical pathway.

IGPD is a recognised novel herbicide target as animals do not have an IGPD

There are two isoforms of IGPD; IGPD1 and IGPD2. The different isoforms are highly conserved with only 8 amino acids differing between them. These subtle differences however affect their activity but as yet it is unknown how.

In most organisms IGPD is a monofunctional protein of about 22 to 29 kD. In some bacteria such as Escherichia coli, it is the C-terminal domain of a bifunctional protein that include a histidinol-phosphatase domain.[1] In E. coli, this is the protein encoded by the hisB gene.[2]

Structural studies[edit]

As of late 2007, 3 structures have been solved for this class of enzymes, with PDB accession codes 1RHY, 2AE8, and 2F1D.

References[edit]

  1. ^ Carlomagno MS, Chiariotti L, Alifano P, Nappo AG, Bruni CB (October 1988). "Structure and function of the Salmonella typhimurium and Escherichia coli K-12 histidine operons". J. Mol. Biol. 203 (3): 585–606. doi:10.1016/0022-2836(88)90194-5. PMID 3062174. 
  2. ^ Brilli, M.; Fani, R. (2004). "Molecular Evolution of hisB Genes". Journal of Molecular Evolution 58 (2): 225–237. doi:10.1007/s00239-003-2547-x. PMID 15042344.  edit

Further reading[edit]

  • AMES BN (1957). "The biosynthesis of histidine; D-erythro-imidazoleglycerol phosphate dehydrase". J. Biol. Chem. 228 (1): 131–43. PMID 13475302. 

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No Pfam abstract.

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000807

Imidazoleglycerol-phosphate dehydratase is the enzyme that catalyses the seventh step in the biosynthesis of histidine in bacteria, fungi and plants. In most organisms it is a monofunctional protein of about 22 to 29 kD. In some bacteria such as Escherichia coli, it is the C-terminal domain of a bifunctional protein that include a histidinol-phosphatase domain [PUBMED:3062174].

Gene Ontology

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Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan S5 (CL0329), which has the following description:

This superfamily contains a wide range of families that possess a structure similar to the second domain of ribosomal S5 protein.

The clan contains the following 14 members:

ChlI DNA_mis_repair EFG_IV Fae GHMP_kinases_N IGPD Lon_C LpxC Ribonuclease_P Ribosomal_S5_C RNase_PH Topo-VIb_trans UPF0029 Xol-1_N

Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(146)
Full
(3695)
Representative proteomes NCBI
(2611)
Meta
(2275)
RP15
(330)
RP35
(666)
RP55
(867)
RP75
(1011)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(146)
Full
(3695)
Representative proteomes NCBI
(2611)
Meta
(2275)
RP15
(330)
RP35
(666)
RP55
(867)
RP75
(1011)
Alignment:
Format:
Order:
Sequence:
Gaps:
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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(146)
Full
(3695)
Representative proteomes NCBI
(2611)
Meta
(2275)
RP15
(330)
RP35
(666)
RP55
(867)
RP75
(1011)
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.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Prosite
Previous IDs: none
Type: Family
Author: Finn RD
Number in seed: 146
Number in full: 3695
Average length of the domain: 144.30 aa
Average identity of full alignment: 51 %
Average coverage of the sequence by the domain: 57.73 %

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 20.3 20.3
Trusted cut-off 20.6 24.1
Noise cut-off 20.2 19.4
Model length: 145
Family (HMM) version: 13
Download: download the raw HMM for this family

Species distribution

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Interactions

There is 1 interaction for this family. More...

IGPD

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 IGPD domain has been found. There are 24 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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