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135  structures 7294  species 0  interactions 8422  sequences 35  architectures

Family: IGPD (PF00475)

Summary: Imidazoleglycerol-phosphate dehydratase

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

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

Imidazoleglycerol-phosphate dehydratase Edit Wikipedia article

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

D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate 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 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.

Structural studies

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


Template:Enzyme references

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

External links

The CAS registry number for this enzyme class is Template:CAS registry.

Template:Enzyme links

Gene Ontology (GO) codes

Template:GO code links

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Imidazoleglycerol-phosphate dehydratase Provide feedback

No Pfam abstract.

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000807

Imidazoleglycerol-phosphate dehydratase (IGPD; EC ) catalyzes the dehydration of imidazole glycerol phosphate to imidazole acetol phosphate, the sixth step of histidine biosynthesis in plants and microorganisms where the histidine is synthesized de novo. There is an internal repeat in the protein domain that is related by pseudo-dyad symmetry, perhaps as a result of an ancient gene duplication. The apo-form of IGPD exists as a catalytically inactive trimer which, in the presence of specific divalent metal cations such as manganese (Mn2+), cobalt (Co2+), cadmium (Cd2+), nickel (Ni2+), iron (Fe2+) and zinc (Zn2+), assembles to form a biologically active high molecular weight metalloenzyme; a 24-mer with 4-3-2 symmetry. Each 24-mer has 24 active sites, and contains around 1.5 metal ions per monomer, each monomer contributing residues to three separate active sites.

IGPD enzymes are monofunctional in fungi, plants, archaea and some eubacteria while they are encoded as bifunctional enzymes in other eubacteria, such that the enzyme is fused to histidinol-phosphate phosphatase, the penultimate enzyme of the histidine biosynthesis pathway. The histidine biosynthesis pathway is a potential target for development of herbicides, and IGPD is a target for the triazole phosphonate herbicides [ PUBMED:16338409 , PUBMED:14724278 , PUBMED:15042344 , PUBMED:10885480 , PUBMED:16511155 , PUBMED:10450980 , PUBMED:8066131 , PUBMED:3001645 , PUBMED:9767718 , PUBMED:8511965 , PUBMED:2664449 , PUBMED:3007936 ].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

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 18 members:

ChlI DNA_gyraseB DNA_mis_repair EFG_IV Fae GalKase_gal_bdg GHMP_kinases_N IGPD Lon_C LpxC Morc6_S5 Ribonuclease_P Ribosomal_S5_C Ribosomal_S9 RNase_PH Topo-VIb_trans UPF0029 Xol-1_N


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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB 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.

Representative proteomes UniProt
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Representative proteomes UniProt

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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.

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

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...


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
Sequence Ontology: SO:0100021
Author: Finn RD
Number in seed: 487
Number in full: 8422
Average length of the domain: 143 aa
Average identity of full alignment: 49 %
Average coverage of the sequence by the domain: 61.05 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 27.0 27.0
Trusted cut-off 27.3 27.4
Noise cut-off 26.8 26.8
Model length: 144
Family (HMM) version: 21
Download: download the raw HMM for this family

Species distribution

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Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence


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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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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 135 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 sequence.

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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A0D2G9X3 View 3D Structure Click here
A0A0H3GV71 View 3D Structure Click here
A0A0R0I5V1 View 3D Structure Click here
A0A0R0KVP9 View 3D Structure Click here
A0A175VVJ5 View 3D Structure Click here
A0A1C1D233 View 3D Structure Click here
A0A1D6DZA5 View 3D Structure Click here
A0JUZ5 View 3D Structure Click here
A0LBT6 View 3D Structure Click here
A0LQG8 View 3D Structure Click here
A0LTS3 View 3D Structure Click here
A0PXP6 View 3D Structure Click here
A0QX83 View 3D Structure Click here
A0RZ75 View 3D Structure Click here
A1A2H5 View 3D Structure Click here
A1ATG7 View 3D Structure Click here
A1B384 View 3D Structure Click here
A1BF00 View 3D Structure Click here
A1KAV7 View 3D Structure Click here
A1R559 View 3D Structure Click here
A1SL60 View 3D Structure Click here
A1T8W3 View 3D Structure Click here
A1TKZ1 View 3D Structure Click here
A1UHK6 View 3D Structure Click here
A1VK39 View 3D Structure Click here
A1W432 View 3D Structure Click here
A1WR21 View 3D Structure Click here
A1WW08 View 3D Structure Click here
A2SE06 View 3D Structure Click here
A3CNT3 View 3D Structure Click here
A3DJF3 View 3D Structure Click here
A3N3W1 View 3D Structure Click here
A3PB03 View 3D Structure Click here
A4FLN6 View 3D Structure Click here
A4G9I9 View 3D Structure Click here
A4J710 View 3D Structure Click here
A4SF66 View 3D Structure Click here
A4VRW2 View 3D Structure Click here
A4X9Q4 View 3D Structure Click here
A4Y087 View 3D Structure Click here