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229  structures 4907  species 2  interactions 17348  sequences 82  architectures

Family: TP_methylase (PF00590)

Summary: Tetrapyrrole (Corrin/Porphyrin) Methylases

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Tetrapyrrole (Corrin/Porphyrin) Methylases Provide feedback

This family uses S-AdoMet in the methylation of diverse substrates. This family includes a related group of bacterial proteins of unknown function, including P45528. This family includes the methylase Dipthine synthase.

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000878

Tetrapyrroles are large macrocyclic compounds derived from a common biosynthetic pathway [PUBMED:11215515]. The end-product, uroporphyrinogen III, is used to synthesise a number of important molecules, including cobalamin (vitamin B12), haem, sirohaem, chlorophyll, coenzyme F430 and phytochromobilin [PUBMED:17227226].

This entry represents several tetrapyrrole methylases, which consist of two non-similar domains. These enzymes catalyse the methylation of their substrates using S-adenosyl-L-methionine as a methyl source. Enzymes in this family include:

  • Uroporphyrinogen III methyltransferase (EC) (SUMT), which catalyses the conversion of uroporphyrinogen III to precorrin-2 at the first branch-point of the tetrapyrrole synthesis pathway, directing the pathway towards cobalamin or sirohaem synthesis [PUBMED:15522295].
  • Precorrin-2 C20-methyltransferase CobI/CbiL (EC), which introduces a methyl group at C-20 on precorrin-2 to produce precorrin-3A during cobalamin biosynthesis. This reaction is key to the conversion of a porphyrin-type tetrapyrrole ring to a corrin ring [PUBMED:17229157]. In some species, this enzyme is part of a bifunctional protein.
  • Precorrin-4 C11-methyltransferase CobM/CbiF (EC), which introduces a methyl group at C-11 on precorrin-4 to produce precorrin-5 during cobalamin biosynthesis [PUBMED:16866557].
  • Sirohaem synthase CysG (EC), domains 4 and 5, which synthesizes sirohaem from uroporphyrinogen III, at the first branch-point in the tetrapyrrole biosynthetic pathway, directing the pathway towards sirohaem synthesis [PUBMED:14595395].
  • Diphthine synthase (EC), which carries out the methylation step during the modification of a specific histidine residue of elongation factor 2 (EF-2) during diphthine synthesis.

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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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
(171)
Full
(17348)
Representative proteomes NCBI
(13595)
Meta
(4640)
RP15
(1545)
RP35
(3155)
RP55
(4100)
RP75
(4809)
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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
(171)
Full
(17348)
Representative proteomes NCBI
(13595)
Meta
(4640)
RP15
(1545)
RP35
(3155)
RP55
(4100)
RP75
(4809)
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
(171)
Full
(17348)
Representative proteomes NCBI
(13595)
Meta
(4640)
RP15
(1545)
RP35
(3155)
RP55
(4100)
RP75
(4809)
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: MRC-LMB Genome group
Previous IDs: none
Type: Domain
Author: Bateman A
Number in seed: 171
Number in full: 17348
Average length of the domain: 206.00 aa
Average identity of full alignment: 21 %
Average coverage of the sequence by the domain: 64.04 %

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 27.3 27.3
Trusted cut-off 27.3 27.4
Noise cut-off 27.1 27.2
Model length: 210
Family (HMM) version: 15
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 2 interactions for this family. More...

TP_methylase CysG_dimeriser

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 TP_methylase domain has been found. There are 229 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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