Summary: Dehydratase large subunit
Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.
The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.
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.
Dehydratase large subunit Provide feedback
This family contains the large subunit of the trimeric diol dehydratases and glycerol dehydratases. These enzymes are produced by some enterobacteria in response to growth substances.
Literature references
-
Tobimatsu T, Azuma M, Hayashi S, Nishimoto K, Toraya T; , Biosci Biotechnol Biochem 1998;62:1774-1777.: Molecular cloning, sequencing and characterization of the genes for adenosylcobalamin-dependent diol dehydratase of Klebsiella pneumoniae. PUBMED:9805380 EPMC:9805380
External database links
SCOP: | 1dio |
This tab holds annotation information from the InterPro database.
InterPro entry IPR003206
This entry represents the large subunit of adenosylcobalamin-dependent diol dehydratases (EC) and glycerol dehydratases (EC). These enzymes are produced by some enterobacteria in response to growth substances. The enzyme have an TIM beta/alpha barrel fold [PUBMED:10903944]. Inactivated holoenzymes are reactivated by their own reactivating factors that mediate the ATP-dependent exchange of an enzyme-bound, damaged cofactor for free adenosylcobalamin through intermediary formation of apoenzyme. The reactivation takes place in two steps: (a) ADP-dependent cobalamin release and (b) ATP-dependent dissociation of the resulting apoenzyme-reactivating factor complexes [PUBMED:17916188].
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
Molecular function | cobalamin binding (GO:0031419) |
hydro-lyase activity (GO:0016836) |
Domain organisation
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
Loading domain graphics...
Pfam Clan
This family is a member of clan Glyco_hydro_tim (CL0058), which has the following description:
This large superfamily contains a range of glycosyl hydrolase enzymes that possess a TIM barrel fold. This CLAN merges clans GH-A, GH-D, GH-H and GH-K from CAZy.
The clan contains the following 58 members:
Alpha-amylase Alpha_L_fucos Cellulase Cellulase-like Dehydratase_LU DUF1906 DUF4015 DUF4038 DUF4434 DUF4838 DUF4849 DUF5010 DUF5696 GHL10 GHL13 GHL15 GHL5 GHL6 Glyco_hydr_30_2 Glyco_hydro_1 Glyco_hydro_10 Glyco_hydro_101 Glyco_hydro_114 Glyco_hydro_129 Glyco_hydro_14 Glyco_hydro_17 Glyco_hydro_18 Glyco_hydro_20 Glyco_hydro_25 Glyco_hydro_26 Glyco_hydro_2_C Glyco_hydro_3 Glyco_hydro_30 Glyco_hydro_31 Glyco_hydro_35 Glyco_hydro_39 Glyco_hydro_42 Glyco_hydro_44 Glyco_hydro_53 Glyco_hydro_56 Glyco_hydro_59 Glyco_hydro_66 Glyco_hydro_70 Glyco_hydro_71 Glyco_hydro_72 Glyco_hydro_77 Glyco_hydro_79n Glyco_hydro_85 Glyco_hydro_97 Glyco_hydro_99 Glyco_hydro_cc Glyco_tran_WbsX hDGE_amylase Melibiase Melibiase_2 NAGidase NAGLU Raffinose_synAlignments
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, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...
View options
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 (25) |
Full (262) |
Representative proteomes | UniProt (1818) |
NCBI (2667) |
Meta (19) |
||||
---|---|---|---|---|---|---|---|---|---|
RP15 (23) |
RP35 (112) |
RP55 (247) |
RP75 (473) |
||||||
Jalview | |||||||||
HTML | |||||||||
PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
not generated,
— not available.
Format an alignment
Download options
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 (25) |
Full (262) |
Representative proteomes | UniProt (1818) |
NCBI (2667) |
Meta (19) |
||||
---|---|---|---|---|---|---|---|---|---|
RP15 (23) |
RP35 (112) |
RP55 (247) |
RP75 (473) |
||||||
Raw Stockholm | |||||||||
Gzipped |
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...
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
Seed source: | Pfam-B_7927 (release 5.2) |
Previous IDs: | none |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Mian N |
Number in seed: | 25 |
Number in full: | 262 |
Average length of the domain: | 520.10 aa |
Average identity of full alignment: | 62 % |
Average coverage of the sequence by the domain: | 93.41 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
|
||||||||||||
Model details: |
|
||||||||||||
Model length: | 552 | ||||||||||||
Family (HMM) version: | 16 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
Sunburst controls
HideWeight segments by...
Change the size of the sunburst
Colour assignments
![]() |
![]() |
![]() |
![]() |
![]() |
![]() |
![]() |
![]() |
Selections
Align selected sequences to HMM
Generate a FASTA-format file
Clear selection
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...
Tree controls
HideThe tree shows the occurrence of this domain across different species. More...
Loading...
Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.
Interactions
There are 4 interactions for this family. More...
Dehydratase_LU Dehydratase_MU Dehydratase_SU Dehydratase_MUStructures
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 Dehydratase_LU domain has been found. There are 32 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.
Loading structure mapping...