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25  structures 1457  species 2  interactions 2367  sequences 35  architectures

Family: Endonuclease_NS (PF01223)

Summary: DNA/RNA non-specific endonuclease

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "DNA/RNA non-specific endonuclease". More...

DNA/RNA non-specific endonuclease Edit Wikipedia article

Endonuclease_NS
PDB 1smn EBI.jpg
identification of the serratia endonuclease dimer: structural basis and implications for catalysis
Identifiers
Symbol Endonuclease_NS
Pfam PF01223
Pfam clan CL0263
InterPro IPR001604
PROSITE PDOC00821
SCOP 1smn
SUPERFAMILY 1smn

In molecular biology, enzymes in the DNA/RNA non-specific endonuclease family of bacterial and eukaryotic endonucleases EC 3.1.30.- share the following characteristics: they act on both DNA and RNA, cleave double-stranded and single-stranded nucleic acids and require a divalent ion such as magnesium for their activity. A histidine has been shown to be essential for the activity of the Serratia marcescens nuclease. This residue is located in a conserved region which also contains an aspartic acid residue that could be implicated in the binding of the divalent ion.[1]

References[edit]

This article incorporates text from the public domain Pfam and InterPro IPR001604

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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.

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No Pfam abstract.

Literature references

  1. Miller MD, Tanner J, Alpaugh M, Benedik MJ, Krause KL; , Nat Struct Biol 1994;1:461-468.: 2.1 A structure of Serratia endonuclease suggests a mechanism for binding to double-stranded DNA. PUBMED:7664065 EPMC:7664065


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001604

A family of bacterial and eukaryotic endonucleases EC share the following characteristics: they act on both DNA and RNA, cleave double-stranded and single-stranded nucleic acids and require a divalent ion such as magnesium for their activity. A histidine has been shown [PUBMED:8078761] to be essential for the activity of the Serratia marcescens nuclease. This residue is located in a conserved region which also contains an aspartic acid residue that could be implicated in the binding of the divalent ion.

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 His-Me_finger (CL0263), which has the following description:

This superfamily defined originally by SCOP contains a diverse range of endonucleases. Later Grishin identified the MH1 domain as belonging to the superfamily [1].

The clan contains the following 19 members:

AHH Colicin-DNase DUF1524 Endonuclea_NS_2 Endonuclease_1 Endonuclease_7 Endonuclease_NS GH-E HNH HNH_2 HNH_3 HNH_4 HNH_5 ICEA LHH MH1 NinG WHH zf-His_Me_endon

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...

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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
(59)
Full
(2367)
Representative proteomes NCBI
(2278)
Meta
(269)
RP15
(233)
RP35
(407)
RP55
(665)
RP75
(866)
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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
(59)
Full
(2367)
Representative proteomes NCBI
(2278)
Meta
(269)
RP15
(233)
RP35
(407)
RP55
(665)
RP75
(866)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(59)
Full
(2367)
Representative proteomes NCBI
(2278)
Meta
(269)
RP15
(233)
RP35
(407)
RP55
(665)
RP75
(866)
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: Prosite
Previous IDs: Endonuclease;
Type: Domain
Author: Finn RD, Bateman A
Number in seed: 59
Number in full: 2367
Average length of the domain: 199.70 aa
Average identity of full alignment: 19 %
Average coverage of the sequence by the domain: 53.76 %

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 20.7 20.7
Trusted cut-off 20.7 20.7
Noise cut-off 20.6 20.5
Model length: 207
Family (HMM) version: 18
Download: download the raw HMM for this family

Species distribution

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Interactions

There are 2 interactions for this family. More...

Endonuclease_NS NuiA

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 Endonuclease_NS domain has been found. There are 25 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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