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8  structures 304  species 0  interactions 844  sequences 4  architectures

Family: Hexose_dehydrat (PF03559)

Summary: NDP-hexose 2,3-dehydratase

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NDP-hexose 2,3-dehydratase Provide feedback

This family includes a range of proteins from antibiotic production pathways. The family includes gra-ORF27 Q9ZA32 product that probably functions at an early step, most likely as a dTDP-4-keto-6- deoxyglucose-2,3-dehydratase [1]. Its homologues include dnmT from the daunorubicin biosynthetic gene cluster in S. peucetius [2] a similar gene from the daunomycin biosynthetic cluster in Streptomyces sp. strain C5 Q53880 [3] , eryBVI from the erythromycin cluster in S. erythraea and snoH from the nogalamycin cluster in S. nogalater. The proteins in this family are composed of two copies of a 200 amino acid long unit that may be a structural domain.

Literature references

  1. Ichinose K, Bedford DJ, Tornus D, Bechthold A, Bibb MJ, Revill WP, Floss HG, Hopwood DA; , Chem Biol 1998;5:647-659.: The granaticin biosynthetic gene cluster of Streptomyces violaceoruber Tu22: sequence analysis and expression in a heterologous host. PUBMED:9831526 EPMC:9831526

  2. Scotti C, Hutchinson CR; , J Bacteriol 1996;178:7316-7321.: Enhanced antibiotic production by manipulation of the Streptomyces peucetius dnrH and dnmT genes involved in doxorubicin (adriamycin) biosynthesis. PUBMED:8955419 EPMC:8955419

  3. Dickens ML, Ye J, Strohl WR; , J Bacteriol 1996;178:3384-3388.: Cloning, sequencing, and analysis of aklaviketone reductase from Streptomyces sp. strain C5. PUBMED:8655529 EPMC:8655529

This tab holds annotation information from the InterPro database.

InterPro entry IPR005212

This domain occurs in a range of proteins from antibiotic production pathways. These include the gra-ORF27 SWISSPROT product that probably functions at an early step, most likely as a dTDP-4-keto-6- deoxyglucose-2,3-dehydratase [ PUBMED:9831526 ]. Its homologues include dnmT from the daunorubicin biosynthetic gene cluster in S. peucetius [ PUBMED:8955419 ], a similar gene from the daunomycin biosynthetic cluster in Streptomyces sp. (strain 5) SWISSPROT [ PUBMED:8655529 ], eryBVI from the erythromycin cluster in S. erythraea and snoH from the nogalamycin cluster in S. nogalater. This domain is a 200 amino acid long region, which may be a structural unit, that occurs twice within the proteins that contain it.

This entry also includes sugar 2,3-dehydratase, EvaA, that belongs to the "Nudix" hydrolase family, members of which often function as "housekeeping" enzymes. EvaA is organised as a dimer, each subunit of the dimer folds into two domains, which are related by a 2-fold rotational axis and which arose via gene duplication. Two binding sites for the dTDP-sugar ligands, pockets A and B, have been identified in each subunit. Site-directed mutagenesis experiments and activity assays strongly suggest that pocket A represents the active site and pocket B is a vestige of the gene duplication event [ PUBMED:23473392 ].

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 NUDIX (CL0261), which has the following description:

This superfamily contains the NUDIX family and one related family.

The clan contains the following 10 members:

DUF4743 DUF4916 Hexose_dehydrat MRP-L46 NUDIX NUDIX-like NUDIX_2 NUDIX_4 NUDIX_5 Nudix_hydro


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.

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Representative proteomes UniProt

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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.

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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: Pfam-B_1070 (release 7.0)
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A
Number in seed: 70
Number in full: 844
Average length of the domain: 199.8 aa
Average identity of full alignment: 38 %
Average coverage of the sequence by the domain: 86.81 %

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 25.0 25.0
Trusted cut-off 25.0 26.1
Noise cut-off 24.9 21.9
Model length: 204
Family (HMM) version: 17
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 Hexose_dehydrat domain has been found. There are 8 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
K0EPP3 View 3D Structure Click here
K0F017 View 3D Structure Click here
Q9ALN6 View 3D Structure Click here