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23  structures 1522  species 0  interactions 2621  sequences 71  architectures

Family: mRNA_cap_enzyme (PF01331)

Summary: mRNA capping enzyme, catalytic domain

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.

mRNA capping enzyme, catalytic domain Provide feedback

This family represents the ATP binding catalytic domain of the mRNA capping enzyme.

Literature references

  1. Hakansson K, Doherty AJ, Shuman S, Wigley DB; , Cell 1997;89:545-553.: X-ray crystallography reveals a large conformational change during guanyl transfer by mRNA capping enzymes. PUBMED:9160746 EPMC:9160746


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001339

This entry represents the adenylation domain of the mRNA capping enzyme [ PUBMED:9160746 ]. The mRNA-capping enzyme is composed of two separate chains alpha and beta, respectively a mRNA guanylyltransferase and an RNA 5'-triphosphatase [ PUBMED:9160746 ]. Binding of the enzyme to nucleotides is specific to the GMP moiety of GTP. The viral mRNA capping enzyme is a monomer that transfers a GMP cap onto the end of mRNA that terminates with a 5'-diphosphate tail.

It contains a catalytic core composed of an adenylation domain and a C-terminal OB-fold domain containing conserved sequence motifs. The adenylation domain binds ATP and contains many active site residues [ PUBMED:11051760 , PUBMED:12820968 ].

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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Pfam Clan

This family is a member of clan DNA_ligase (CL0078), which has the following description:

This superfamily contains both ATP-dependent and NAD dependent DNA ligase enzymes. The family also includes mRNA capping enzymes. The members of this clan were shown to be related by sequence in [1].

The clan contains the following 5 members:

DNA_ligase_A_M DNA_ligase_aden mRNA_cap_enzyme PNKP_ligase RNA_ligase

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
(8)
Full
(2621)
Representative proteomes UniProt
(4471)
RP15
(594)
RP35
(1262)
RP55
(2039)
RP75
(2722)
Jalview View  View  View  View  View  View  View 
HTML View  View           
PP/heatmap 1 View           

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

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

Format an alignment

  Seed
(8)
Full
(2621)
Representative proteomes UniProt
(4471)
RP15
(594)
RP35
(1262)
RP55
(2039)
RP75
(2722)
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
(8)
Full
(2621)
Representative proteomes UniProt
(4471)
RP15
(594)
RP35
(1262)
RP55
(2039)
RP75
(2722)
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: Sarah Teichmann
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Finn RD , Bateman A , Griffiths-Jones SR
Number in seed: 8
Number in full: 2621
Average length of the domain: 175.5 aa
Average identity of full alignment: 36 %
Average coverage of the sequence by the domain: 34.28 %

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 29.6 29.6
Trusted cut-off 29.7 29.6
Noise cut-off 29.5 29.5
Model length: 195
Family (HMM) version: 22
Download: download the raw HMM for this family

Species distribution

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Colour assignments

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

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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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 mRNA_cap_enzyme domain has been found. There are 23 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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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
A0A044U6U6 View 3D Structure Click here
A0A077YZB8 View 3D Structure Click here
A0A077Z2R0 View 3D Structure Click here
A0A0D2GH49 View 3D Structure Click here
A0A0K0EI86 View 3D Structure Click here
A0A0K0J3S1 View 3D Structure Click here
A0A0N4UCR5 View 3D Structure Click here
A0A0R0KQX0 View 3D Structure Click here
A0A183XJR9 View 3D Structure Click here
A0A1C1CCR0 View 3D Structure Click here
A0A1D6EGX8 View 3D Structure Click here
A0A1D8PME6 View 3D Structure Click here
A0A5K4FAB6 View 3D Structure Click here
A4I7V3 View 3D Structure Click here
C0NLY6 View 3D Structure Click here
C0PFH1 View 3D Structure Click here
C1GVF0 View 3D Structure Click here
D3ZH30 View 3D Structure Click here
F4IYM6 View 3D Structure Click here
I1KKA0 View 3D Structure Click here
I1N9F9 View 3D Structure Click here
K7K355 View 3D Structure Click here
K7KDH1 View 3D Structure Click here
K7MTE7 View 3D Structure Click here
O55236 View 3D Structure Click here
O60942 View 3D Structure Click here
P40997 View 3D Structure Click here
Q01159 View 3D Structure Click here
Q17607 View 3D Structure Click here
Q2QWJ7 View 3D Structure Click here
Q381X9 View 3D Structure Click here
Q4D3H7 View 3D Structure Click here
Q4DNJ8 View 3D Structure Click here
Q54HV6 View 3D Structure Click here
Q6BT58 View 3D Structure Click here
Q6C783 View 3D Structure Click here
Q6CWR0 View 3D Structure Click here
Q6FQ31 View 3D Structure Click here
Q6NY98 View 3D Structure Click here
Q755D0 View 3D Structure Click here