!!

Powering down the Pfam website
On October 5th, we will start redirecting the traffic from Pfam (pfam.xfam.org) to InterPro (www.ebi.ac.uk/interpro). The Pfam website will be available at pfam-legacy.xfam.org until January 2023, when it will be decommissioned. You can read more about the sunset period in our blog post.

Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
2  structures 2052  species 0  interactions 7426  sequences 191  architectures

Family: Gly_transf_sug (PF04488)

Summary: Glycosyltransferase sugar-binding region containing DXD motif

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 "Clostridial Cytotoxin family". More...

Clostridial Cytotoxin family Edit Wikipedia article

The Clostridial Cytotoxin (CCT) Family (TC# 1.C.57) is a member of the RTX-toxin superfamily. There are currently 13 classified members belonging to the CCT family. A list of these proteins is available in the Transporter Classification Database. Homologues are found in a variety of Gram-positive and Gram-negative bacteria.

Clostridial difficile cytotoxins

Clostridium difficile, the causative agent of nosocomial antibiotic-associated diarrhea and pseudomembranous colitis, possesses two main virulence factors: the large clostridial cytotoxins A (TcdA) and B (TcdB). Cleavage of toxin B and all other large clostridial cytotoxins, is an autocatalytic process dependent on host cytosolic inositolphosphate cofactors. A covalent inhibitor of aspartate proteases, 1,2-epoxy-3-(p-nitrophenoxy)propane, completely blocks toxin B function on cultured cells and was used to identify the catalytically active protease site. The toxin uses eukaryotic signals for induced autoproteolysis to deliver its toxic domain into the cytosol of target cells. Reineke et al. (2007) present an integrated model for the uptake and inositolphosphate-induced activation of toxin B.

Clostridium difficile infection, caused by the actions of the homologous toxins TcdA and TcdB on colonic epithelial cells is due to binding to target cells which triggers toxin internalization into acidified vesicles, whereupon cryptic segments from within the 1,050-aa translocation domain unfurl and insert into the bounding membrane, creating a transmembrane passageway to the cytosol (Zhang et al. 2014). Sensitive residues-clustered between amino acyl residues 1,035 and 1,107, when individually mutated, reduced cellular toxicity by >1,000-fold. Defective variants exhibit impaired pore formation in planar lipid bilayers and biological membranes, resulting in an inability to intoxicate cells through either apoptotic or necrotic pathways. The findings suggest similarities between the pore- forming 'hotspots' of TcdB and the diphtheria toxin translocation domain (Zhang et al. 2014).

Function

Two of the more well known model members of the CCT family are clostridial cytotoxins A and B. Proteolytically processed clostridial cytotoxins A (306 kDa; TC# 1.C.57.1.2) and B (269 kDa; TC# 1.C.57.1.1) are O-glycosyltransferases that modify small GTPases of the Rho family by glucosylation of threonine residues, thereby blocking the action of the GTPases as switches of signal processes such as those mediated by the actin cytoskeleton. The toxins thus induce redistribution of actin filaments and cause the cells to round up. The catalytic domains of CCTs probably enter the cytoplasm from acidic endosomes. The toxins form ion-permeable channels in cell membranes and artificial bilayers when exposed to acidic pH. pH-dependent channel formation has been demonstrated for C. difficile Toxin B and C as well as sordelli lethal toxin. Low pH presumably induces conformational/structural changes that promote membrane insertion and channel formation.

Structure

These cytotoxins are large (e.g., toxin B of C. difficile is 2366 aas long) and tripartite with the N-terminal domain being the catalytic unit, the C-terminal domain being the cellular receptor and the central hydrophobic domain being the channel-former. In this respect, they superficially resemble diphtheria toxin (BT; 1.C.7) although no significant sequence similarity between CCTs and BT is observed. The E. coli toxin B protein and the Chlamydial TC0437 protein are of 3169 aas and 3255 aas, respectively. The distantly related ToxA toxin of Pasteurella multocida is 1285 aas while the E. coli Cnf1 and 2 toxins are 1014 aas, and the RTX cytotoxin of Vibrio vulnificus is 5206 aas.

Large Clostridial Toxins

Clostridium difficile toxins A and B are members of an important class of virulence factors known as large clostridial toxins (LCTs). Toxin action involves four major steps:

  1. receptor-mediated endocytosis
  2. translocation of a catalytic glucosyltransferase domain across the membrane
  3. release of the enzymatic moiety by autoproteolytic processing
  4. and a glucosyltransferase-dependent inactivation of Rho family proteins.

Pruitt et al. (2010) have imaged toxin A (TcdA) and toxin B (TcdB) holotoxins by negative stain electron microscopy to show that these molecules are similar in structure. They then determined a 3D structure for TcdA and mapped the organization of its functional domains. The molecule has a 'pincher-like' head corresponding to the delivery domain and two tails, long and short, corresponding to the receptor-binding and glucosyltransferase domains, respectively. A second structure, obtained at the acidic pH of an endosome, reveals a significant structural change in the delivery and glucosyltransferase domains, and thus provides a framework for understanding the molecular mechanism of LCT cellular intoxication (Pruitt et al., 2010).

Transport Reaction

The generalized transport reactions catalyzed by CCTs are:

N-terminal catalytic domain (out) → N-terminal catalytic domain (in)
Ions and other solutes (in) → Ions and other solutes (out)

See Also


References

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.

Glycosyltransferase sugar-binding region containing DXD motif Provide feedback

The DXD motif is a short conserved motif found in many families of glycosyltransferases, which add a range of different sugars to other sugars, phosphates and proteins. DXD-containing glycosyltransferases all use nucleoside diphosphate sugars as donors and require divalent cations, usually manganese. The DXD motif is expected to play a carbohydrate binding role in sugar-nucleoside diphosphate and manganese dependent glycosyltransferases [1].

Literature references

  1. Wiggins CA, Munro S; , Proc Natl Acad Sci U S A 1998;95:7945-7950.: Activity of the yeast MNN1 alpha-1,3-mannosyltransferase requires a motif conserved in many other families of glycosyltransferases. PUBMED:9653120 EPMC:9653120


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR007577

This entry represents those sugar-binding regions of glycosyltransferases that contain a DXD motif. The DXD motif is a short conserved motif found in many families of glycosyltransferases, which add a range of different sugars to other sugars, phosphates and proteins. DXD-containing glycosyltransferases all use nucleoside diphosphate sugars as donors and require divalent cations, usually manganese. The DXD motif is expected to play a carbohydrate binding role in sugar-nucleoside diphosphate and manganese dependent glycosyltransferases [ PUBMED:9653120 ].

Domain organisation

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

Loading domain graphics...

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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB 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
(21)
Full
(7426)
Representative proteomes UniProt
(16998)
RP15
(1632)
RP35
(3560)
RP55
(5814)
RP75
(8666)
Jalview View  View  View  View  View  View  View 
HTML View             
PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(21)
Full
(7426)
Representative proteomes UniProt
(16998)
RP15
(1632)
RP35
(3560)
RP55
(5814)
RP75
(8666)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

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
(21)
Full
(7426)
Representative proteomes UniProt
(16998)
RP15
(1632)
RP35
(3560)
RP55
(5814)
RP75
(8666)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped 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.

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: DOMO:DM04307;
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Kerrison ND
Number in seed: 21
Number in full: 7426
Average length of the domain: 98.5 aa
Average identity of full alignment: 21 %
Average coverage of the sequence by the domain: 23.1 %

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 23.0 23.0
Trusted cut-off 23.0 23.0
Noise cut-off 22.9 22.9
Model length: 98
Family (HMM) version: 18
Download: download the raw HMM for this family

Species distribution

Sunburst controls

Hide

Weight segments by...


Change the size of the sunburst

Small
Large

Colour assignments

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

Selections

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...

Loading sunburst data...

Tree controls

Hide

The 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.

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 Gly_transf_sug domain has been found. There are 2 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...

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
A0A0D2FCP6 View 3D Structure Click here
A0A0D2G3Y7 View 3D Structure Click here
A0A0D2G4D2 View 3D Structure Click here
A0A0D2G6Z5 View 3D Structure Click here
A0A175VSU4 View 3D Structure Click here
A0A175VXL9 View 3D Structure Click here
A0A175VY90 View 3D Structure Click here
A0A175W191 View 3D Structure Click here
A0A175W9C3 View 3D Structure Click here
A0A175WEB3 View 3D Structure Click here
A0A1C1CDI6 View 3D Structure Click here
A0A1C1CHT2 View 3D Structure Click here
A0A1C1D1W0 View 3D Structure Click here
A0A1C1D1W8 View 3D Structure Click here
A0A1D6IGU1 View 3D Structure Click here
A0A1D8PIF7 View 3D Structure Click here
A0A1D8PPM7 View 3D Structure Click here
A0A1P8APP1 View 3D Structure Click here
C0NX82 View 3D Structure Click here
C0P0M3 View 3D Structure Click here
C1GXF1 View 3D Structure Click here
C1GZV7 View 3D Structure Click here
C1H5E2 View 3D Structure Click here
C1H7W6 View 3D Structure Click here
C1HAX2 View 3D Structure Click here
D3ZG90 View 3D Structure Click here
F4IS00 View 3D Structure Click here
F4IS01 View 3D Structure Click here
I1M279 View 3D Structure Click here
K7K379 View 3D Structure Click here
K7L1S4 View 3D Structure Click here
K7L365 View 3D Structure Click here
K7N0U6 View 3D Structure Click here
K7TM90 View 3D Structure Click here
O14084 View 3D Structure Click here
P0C8Q4 View 3D Structure Click here
P31755 View 3D Structure Click here
P33300 View 3D Structure Click here
P38287 View 3D Structure Click here
P47124 View 3D Structure Click here