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180  structures 5352  species 0  interactions 14979  sequences 243  architectures

Family: NTP_transf_2 (PF01909)

Summary: Nucleotidyltransferase domain

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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.

Nucleotidyltransferase domain Provide feedback

Members of this family belong to a large family of nucleotidyltransferases [1]. This family includes kanamycin nucleotidyltransferase (KNTase) which is a plasmid-coded enzyme responsible for some types of bacterial resistance to aminoglycosides. KNTase in-activates antibiotics by catalysing the addition of a nucleotidyl group onto the drug.

Literature references

  1. Holm L, Sander C; , Trends Biochem Sci 1995;20:345-347.: DNA polymerase beta belongs to an ancient nucleotidyltransferase superfamily. PUBMED:7482698 EPMC:7482698


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR002934

A small region that overlaps with a nuclear localization signal and binds to the RNA primer contains three aspartates that are essential for catalysis. Sequence and secondary structure comparisons of regions surrounding these aspartates with sequences of other polymerases revealed a significant homology to the palm structure of DNA polymerase beta, terminal deoxynucleotidyltransferase and DNA polymerase IV of Saccharomyces cerevisiae, all members of the family X of polymerases. This homology extends as far as cca: tRNA nucleotidyltransferase and streptomycin adenylyltransferase, an antibiotic resistance factor [ PUBMED:7482698 , PUBMED:8665867 ].

Proteins containing this domain include kanamycin nucleotidyltransferase (KNTase) which is a plasmid-coded enzyme responsible for some types of bacterial resistance to aminoglycosides. KNTase inactivates antibiotics by catalysing the addition of a nucleotidyl group onto the drug. In experiments, Mn2+ strongly stimulated this reaction due to a 50-fold lower Ki for 8-azido-ATP in the presence of Mn2+. Mutations of the highly conserved Asp residues 113, 115, and 167, critical for metal binding in the catalytic domain of bovine poly(A) polymerase, led to a strong reduction of cross-linking efficiency, and Mn2+ no longer stimulated the reaction. Mutations in the region of the "helical turn motif" (a domain binding the triphosphate moiety of the nucleotide) and in the suspected nucleotide-binding helix of bovine poly(A) polymerase impaired ATP binding and catalysis. The results indicate that ATP is bound in part by the helical turn motif and in part by a region that may be a structural analogue of the fingers domain found in many polymerases.

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

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
(67)
Full
(14979)
Representative proteomes UniProt
(61165)
RP15
(2304)
RP35
(7008)
RP55
(13651)
RP75
(21927)
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
(67)
Full
(14979)
Representative proteomes UniProt
(61165)
RP15
(2304)
RP35
(7008)
RP55
(13651)
RP75
(21927)
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
(67)
Full
(14979)
Representative proteomes UniProt
(61165)
RP15
(2304)
RP35
(7008)
RP55
(13651)
RP75
(21927)
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: [1]
Previous IDs: DUF76;
Type: Family
Sequence Ontology: SO:0100021
Author: Bateman A
Number in seed: 67
Number in full: 14979
Average length of the domain: 96.90 aa
Average identity of full alignment: 16 %
Average coverage of the sequence by the domain: 19.67 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.0 21.0
Trusted cut-off 21.0 21.0
Noise cut-off 20.9 20.9
Model length: 94
Family (HMM) version: 25
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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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 NTP_transf_2 domain has been found. There are 180 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
A0A096PQM6 View 3D Structure Click here
A0A096RRB4 View 3D Structure Click here
A0A0G2JZ04 View 3D Structure Click here
A0A0G2K0C9 View 3D Structure Click here
A0A0G2K239 View 3D Structure Click here
A0A0N7KP35 View 3D Structure Click here
A0A0P0WXU0 View 3D Structure Click here
A0A0R0EJS3 View 3D Structure Click here
A0A0R0KL49 View 3D Structure Click here
A0A1D6E1L2 View 3D Structure Click here
A0A1D6GKT2 View 3D Structure Click here
A0A1D6H5B7 View 3D Structure Click here
A0A1D6INW1 View 3D Structure Click here
A0A1D6KIM6 View 3D Structure Click here
A0A1D6KZ09 View 3D Structure Click here
A0A1D6LPX6 View 3D Structure Click here
A0A1D6MNC4 View 3D Structure Click here
A0A1D6NLA1 View 3D Structure Click here
A0A1D6P1T9 View 3D Structure Click here
A0A1D6QGJ6 View 3D Structure Click here
A0A1D6UPT1 View 3D Structure Click here
A0A2R8QS61 View 3D Structure Click here
A0A5K1K8X2 View 3D Structure Click here
A2BGL0 View 3D Structure Click here
A4HW64 View 3D Structure Click here
A4I1X5 View 3D Structure Click here
A4ICZ6 View 3D Structure Click here
B7F8L5 View 3D Structure Click here
C6KT92 View 3D Structure Click here
D3ZAN6 View 3D Structure Click here
D3ZSY1 View 3D Structure Click here
E9Q9A9 View 3D Structure Click here
F4JFF2 View 3D Structure Click here
F4JH01 View 3D Structure Click here
G5EBX5 View 3D Structure Click here
G5EFL0 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
K7KV26 View 3D Structure Click here
K7KZ14 View 3D Structure Click here
K7L0R9 View 3D Structure Click here
K7MXG4 View 3D Structure Click here
K7VMF5 View 3D Structure Click here
K7WFZ8 View 3D Structure Click here
O13798 View 3D Structure Click here
O13833 View 3D Structure Click here
O44768 View 3D Structure Click here
O74326 View 3D Structure Click here
O82312 View 3D Structure Click here
P00973 View 3D Structure Click here
P04053 View 3D Structure Click here
P09838 View 3D Structure Click here
P11928 View 3D Structure Click here
P27249 View 3D Structure Click here
P29468 View 3D Structure Click here
P29728 View 3D Structure Click here
P48561 View 3D Structure Click here
P51003 View 3D Structure Click here
P53632 View 3D Structure Click here
Q05961 View 3D Structure Click here
Q09995 View 3D Structure Click here
Q10295 View 3D Structure Click here
Q20377 View 3D Structure Click here
Q4CV31 View 3D Structure Click here
Q4D666 View 3D Structure Click here
Q4DA83 View 3D Structure Click here
Q54J73 View 3D Structure Click here
Q555M9 View 3D Structure Click here
Q57590 View 3D Structure Click here
Q57592 View 3D Structure Click here
Q57606 View 3D Structure Click here
Q57877 View 3D Structure Click here
Q58021 View 3D Structure Click here
Q58486 View 3D Structure Click here
Q58511 View 3D Structure Click here
Q58612 View 3D Structure Click here
Q58614 View 3D Structure Click here
Q58701 View 3D Structure Click here
Q58774 View 3D Structure Click here
Q5A2B2 View 3D Structure Click here
Q5BKD0 View 3D Structure Click here
Q5BPR8 View 3D Structure Click here
Q5MYT7 View 3D Structure Click here
Q5MYU0 View 3D Structure Click here
Q5MYX1 View 3D Structure Click here
Q5SNY2 View 3D Structure Click here
Q5TAX3 View 3D Structure Click here
Q5XG87 View 3D Structure Click here
Q61183 View 3D Structure Click here
Q68ED3 View 3D Structure Click here
Q6H5Y8 View 3D Structure Click here
Q6PB75 View 3D Structure Click here
Q6PCL9 View 3D Structure Click here
Q7KVS9 View 3D Structure Click here
Q7XN15 View 3D Structure Click here
Q84WU1 View 3D Structure Click here
Q8K469 View 3D Structure Click here
Q8NDF8 View 3D Structure Click here
Q8VI93 View 3D Structure Click here
Q8VI97 View 3D Structure Click here
Q8VYW1 View 3D Structure Click here
Q9BWT3 View 3D Structure Click here
Q9LMT2 View 3D Structure Click here
Q9NRJ5 View 3D Structure Click here
Q9U2P3 View 3D Structure Click here
Q9UTN3 View 3D Structure Click here
Q9UW26 View 3D Structure Click here
Q9VC07 View 3D Structure Click here
Q9WVP6 View 3D Structure Click here
Q9Y6K5 View 3D Structure Click here