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15  structures 1504  species 0  interactions 5106  sequences 73  architectures

Family: PAP_RNA-bind (PF04926)

Summary: Poly(A) polymerase predicted RNA binding domain

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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.

Poly(A) polymerase predicted RNA binding domain Provide feedback

Based on its similarity structurally to the RNA recognition motif this domain is thought to be RNA binding [1].

Literature references

  1. Martin G, Keller W, Doublie S; , EMBO J 2000;19:4193-4203.: Crystal structure of mammalian poly(A) polymerase in complex with an analog of ATP. PUBMED:10944102 EPMC:10944102


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR007010

In eukaryotes, polyadenylation of pre-mRNA plays an essential role in the initiation step of protein synthesis, as well as in the export and stability of mRNAs. Poly(A) polymerase, the enzyme at the heart of the polyadenylation machinery, is a template-independent RNA polymerase that specifically incorporates ATP at the 3' end of mRNA. The crystal structure of bovine poly(A) polymerase bound to an ATP analogue at 2.5 A resolution has been determined [ PUBMED:10944102 ]. The structure revealed expected and unexpected similarities to other proteins. As expected, the catalytic domain of poly(A) polymerase shares substantial structural homology with other nucleotidyl transferases such as DNA polymerase beta and kanamycin transferase.

The C-terminal domain unexpectedly folds into a compact domain reminiscent of the RNA-recognition motif fold. The three invariant aspartates of the catalytic triad ligate two of the three active site metals. One of these metals also contacts the adenine ring. Furthermore, conserved, catalytically important residues contact the nucleotide. These contacts, taken together with metal coordination of the adenine base, provide a structural basis for ATP selection by poly(A) polymerase.

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 (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
(100)
Full
(5106)
Representative proteomes UniProt
(7844)
RP15
(757)
RP35
(2039)
RP55
(3845)
RP75
(5291)
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
(100)
Full
(5106)
Representative proteomes UniProt
(7844)
RP15
(757)
RP35
(2039)
RP55
(3845)
RP75
(5291)
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
(100)
Full
(5106)
Representative proteomes UniProt
(7844)
RP15
(757)
RP35
(2039)
RP55
(3845)
RP75
(5291)
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: Pfam-B_1341 (release 7.6)
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Wood V , Bateman A
Number in seed: 100
Number in full: 5106
Average length of the domain: 92 aa
Average identity of full alignment: 25 %
Average coverage of the sequence by the domain: 18.92 %

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 24.0 24.0
Trusted cut-off 24.0 24.0
Noise cut-off 23.9 23.9
Model length: 187
Family (HMM) version: 18
Download: download the raw HMM for this family

Species distribution

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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 PAP_RNA-bind domain has been found. There are 15 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
A0A044UFT9 View 3D Structure Click here
A0A077ZF29 View 3D Structure Click here
A0A096RRB4 View 3D Structure Click here
A0A0D2HJS0 View 3D Structure Click here
A0A0G2K0C9 View 3D Structure Click here
A0A0K0DU80 View 3D Structure Click here
A0A0K0JMS6 View 3D Structure Click here
A0A0N4U1C8 View 3D Structure Click here
A0A0P0WY39 View 3D Structure Click here
A0A175VWC4 View 3D Structure Click here
A0A1C1CMA6 View 3D Structure Click here
A0A1D6E1L2 View 3D Structure Click here
A0A1D6GKT2 View 3D Structure Click here
A0A1D6KZ09 View 3D Structure Click here
A0A1D6P1T9 View 3D Structure Click here
A0A1D6QQ32 View 3D Structure Click here
A0A3P7F7M4 View 3D Structure Click here
A0A3Q0KTL7 View 3D Structure Click here
A0A5S6PS30 View 3D Structure Click here
A2BGL0 View 3D Structure Click here
A4HW64 View 3D Structure Click here
B7F8L5 View 3D Structure Click here
C0NER3 View 3D Structure Click here
C1H3L1 View 3D Structure Click here
C6KT92 View 3D Structure Click here
D3ZAN6 View 3D Structure Click here
G5EBX5 View 3D Structure Click here
I1K9H3 View 3D Structure Click here
I1KV14 View 3D Structure Click here
I1L486 View 3D Structure Click here
K7KIY8 View 3D Structure Click here
K7KZ14 View 3D Structure Click here
K7L0R9 View 3D Structure Click here
O82312 View 3D Structure Click here
P25500 View 3D Structure Click here
P29468 View 3D Structure Click here
P51003 View 3D Structure Click here
Q09995 View 3D Structure Click here
Q10295 View 3D Structure Click here
Q4DA83 View 3D Structure Click here