Summary: Transglutaminase-like superfamily
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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
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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
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Pfister P, Wasserfallen A, Stettler R, Leisinger T; , Mol Microbiol 1998;30:233-244.: Molecular analysis of Methanobacterium phage psiM2. PUBMED:9791169 EPMC:9791169
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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
Internal database links
SCOOP: | Acetyltransf_2 DUF553 EDR1 Peptidase_C71 Peptidase_C93 Rad4 Transglut_core3 |
Similarity to PfamA using HHSearch: | DUF553 Transglut_core3 EDR1 |
External database links
HOMSTRAD: | Transglut_core Transglutamin_NC |
PROSITE: | PDOC00473 |
SCOP: | 1fie |
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 homologues 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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Pfam Clan
This family is a member of clan Peptidase_CA (CL0125), which has the following description:
This clan includes peptidases with the papain-like fold.
The clan contains the following 74 members:
Acetyltransf_2 Amidase_5 Amidase_6 BtrH_N CHAP CIF CoV_peptidase DUF1175 DUF1287 DUF1460 DUF2026 DUF2272 DUF3335 DUF553 EDR1 Gln_deamidase_2 Guanylate_cyc_2 Herpes_teg_N Josephin LRAT Mac-1 Menin NLPC_P60 Nt_Gln_amidase OTU Peptidase_C1 Peptidase_C10 Peptidase_C101 Peptidase_C12 Peptidase_C16 Peptidase_C1_2 Peptidase_C2 Peptidase_C21 Peptidase_C23 Peptidase_C27 Peptidase_C28 Peptidase_C31 Peptidase_C32 Peptidase_C33 Peptidase_C34 Peptidase_C36 Peptidase_C39 Peptidase_C39_2 Peptidase_C42 Peptidase_C47 Peptidase_C48 Peptidase_C5 Peptidase_C54 Peptidase_C58 Peptidase_C6 Peptidase_C65 Peptidase_C7 Peptidase_C70 Peptidase_C71 Peptidase_C78 Peptidase_C8 Peptidase_C9 Peptidase_C92 Peptidase_C93 Peptidase_C97 Peptidase_C98 Phytochelatin Rad4 SidE_DUB Tae4 TGase_elicitor Tox-PLDMTX Transglut_core Transglut_core2 Transglut_core3 Transglut_prok UCH UCH_1 VasohibinAlignments
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...
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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.
Seed (83) |
Full (20604) |
Representative proteomes | UniProt (78690) |
NCBI (117487) |
Meta (1020) |
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RP15 (2572) |
RP35 (9537) |
RP55 (19792) |
RP75 (33617) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
not generated,
— not available.
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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.
Seed (83) |
Full (20604) |
Representative proteomes | UniProt (78690) |
NCBI (117487) |
Meta (1020) |
||||
---|---|---|---|---|---|---|---|---|---|
RP15 (2572) |
RP35 (9537) |
RP55 (19792) |
RP75 (33617) |
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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: | [1] |
Previous IDs: | none |
Type: | Family |
Sequence Ontology: | SO:0100021 |
Author: |
Bateman A |
Number in seed: | 83 |
Number in full: | 20604 |
Average length of the domain: | 111.40 aa |
Average identity of full alignment: | 19 % |
Average coverage of the sequence by the domain: | 19.66 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 112 | ||||||||||||
Family (HMM) version: | 20 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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Selections
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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 5 interactions for this family. More...
Transglut_N Transglut_core Transglut_N Transglut_C Transglut_CStructures
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 65 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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