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45  structures 2577  species 3  interactions 6914  sequences 194  architectures

Family: Transglut_core (PF01841)

Summary: Transglutaminase-like superfamily

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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.

Transglutaminase-like superfamily Provide feedback

This family includes animal transglutaminases and other bacterial proteins of unknown function. Sequence conservation in this superfamily primarily involves three motifs that centre around conserved cysteine, histidine, and aspartate residues that form the catalytic triad in the structurally characterised transglutaminase, the human blood clotting factor XIIIa' [1]. On the basis of the experimentally demonstrated activity of the Methanobacterium phage pseudomurein endoisopeptidase [2] it is proposed that many, if not all, microbial homologues of the transglutaminases are proteases and that the eukaryotic transglutaminases have evolved from an ancestral protease. [3]

Literature references

  1. Yee VC, Pedersen LC, Le Trong I, Bishop PD, Stenkamp RE, Teller DC; , Proc Natl Acad Sci USA 1994;91:7296-7300.: Three-dimensional structure of a transglutaminase: human blood coagulation factor XIII. PUBMED:7913750 EPMC:7913750

  2. Pfister P, Wasserfallen A, Stettler R, Leisinger T; , Mol Microbiol 1998;30:233-244.: Molecular analysis of Methanobacterium phage psiM2. PUBMED:9791169 EPMC:9791169

  3. Makarova KS, Aravind L, Koonin EV; , Protein Sci 1999;8:1714-1719.: A superfamily of archaeal, bacterial, and eukaryotic proteins homologous to animal transglutaminases [In Process Citation] PUBMED:10452618 EPMC:10452618


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR002931

This domain is found in many proteins known to have transglutaminase activity, i.e. which cross-link proteins through an acyl-transfer reaction between the gamma-carboxamide group of peptide-bound glutamine and the epsilon-amino group of peptide-bound lysine, resulting in a epsilon-(gamma-glutamyl)lysine isopeptide bond. Tranglutaminases have been found in a diverse range of species, from bacteria through to mammals. The enzymes require calcium binding and their activity leads to post-translational modification of proteins through acyl-transfer reactions, involving peptidyl glutamine residues as acyl donors and a variety of primary amines as acyl acceptors, with the generation of proteinase resistant isopeptide bonds [PUBMED:12366374].

Sequence conservation in this superfamily primarily involves three motifs that centre around conserved cysteine, histidine, and aspartate residues that form the catalytic triad in the structurally characterised transglutaminase, the human blood clotting factor XIIIa' [PUBMED:7913750]. On the basis of the experimentally demonstrated activity of the Methanobacterium phage psiM2 pseudomurein endoisopeptidase [PUBMED:9791169], it is proposed that many, if not all, microbial homologs of the transglutaminases are proteases and that the eukaryotic transglutaminases have evolved from an ancestral protease [PUBMED:10452618].

A subunit of plasma Factor XIII revealed that each Factor XIIIA subunit is composed of four domains (termed N-terminal beta-sandwich, core domain (containing the catalytic and the regulatory sites), and C-terminal beta-barrels 1 and 2) and that two monomers assemble into the native dimer through the surfaces in domains 1 and 2, in opposite orientation. This organisation in four domains is highly conserved during evolution among transglutaminase isoforms [PUBMED:12366374].

Domain organisation

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

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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...

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
(87)
Full
(6914)
Representative proteomes NCBI
(6853)
Meta
(1021)
RP15
(827)
RP35
(1630)
RP55
(2120)
RP75
(2597)
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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
(87)
Full
(6914)
Representative proteomes NCBI
(6853)
Meta
(1021)
RP15
(827)
RP35
(1630)
RP55
(2120)
RP75
(2597)
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
(87)
Full
(6914)
Representative proteomes NCBI
(6853)
Meta
(1021)
RP15
(827)
RP35
(1630)
RP55
(2120)
RP75
(2597)
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: [1]
Previous IDs: none
Type: Family
Author: Bateman A
Number in seed: 87
Number in full: 6914
Average length of the domain: 111.30 aa
Average identity of full alignment: 20 %
Average coverage of the sequence by the domain: 20.05 %

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 21.8 21.8
Trusted cut-off 21.8 21.8
Noise cut-off 21.7 21.7
Model length: 113
Family (HMM) version: 14
Download: download the raw HMM for this family

Species distribution

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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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Interactions

There are 3 interactions for this family. More...

Transglut_C Transglut_core Transglut_N

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 Transglut_core domain has been found. There are 45 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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