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349  structures 4592  species 0  interactions 14812  sequences 161  architectures

Family: SNase (PF00565)

Summary: Staphylococcal nuclease homologue

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 "Micrococcal nuclease". More...

Micrococcal nuclease Edit Wikipedia article

Micrococcal Nuclease (S7 Nuclease) is a relatively nonspecific endo-exonuclease that digests single-stranded and double-stranded nucleic acids, but is more active on single-stranded substrates. Cleavage of DNA or RNA occurs preferentially at AT or AU-rich regions yielding mononucleotides and oligonucleotides with terminal 3'-phosphates. The enzyme activity is strictly dependent on Ca2+.

Source E.coli cells carrying a cloned nuc gene encoding Staphylococcus aureus extracellular nuclease (micrococcal nuclease).

Applications Hydrolysis of nucleic acids in crude cell-free extracts. Sequencing of RNA . Studies of chromatin structure. A model for protein folding and for structure-function studies

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.

Staphylococcal nuclease homologue Provide feedback

Present in all three domains of cellular life. Four copies in the transcriptional coactivator p100: these, however, appear to lack the active site residues of Staphylococcal nuclease. Positions 14 (Asp-21), 34 (Arg-35), 39 (Asp-40), 42 (Glu-43) and 110 (Arg-87) [SNase numbering in parentheses] are thought to be involved in substrate-binding and catalysis.

Literature references

  1. Ponting CP; , Protein Sci 1997;6:459-463.: P100, a transcriptional coactivator, is a human homologue of staphylococcal nuclease. PUBMED:9041650 EPMC:9041650

  2. Callebaut I, Mornon JP; , Biochem J 1997;321:125-132.: The human EBNA-2 coactivator p100: multidomain organization and relationship to the staphylococcal nuclease fold and to the tudor protein involved in Drosophila melanogaster development. PUBMED:9003410 EPMC:9003410


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR016071

Staphylococcus aureus nuclease (SNase) homologues, previously thought to be restricted to bacteria and archaea, are also in eukaryotes. Staphylococcal nuclease has a multi-domain organisation [ PUBMED:9003410 ]. The human cellular coactivator p100 contains four repeats, each of which is a SNase homologue. These repeats are unlikely to possess SNase-like activities as each lacks equivalent SNase catalytic residues, yet they may mediate p100's single-stranded DNA-binding function [ PUBMED:9041650 ]. A variety of proteins including many that are still uncharacterised belong to this group.

SNase domains have an OB-fold consisting of a closed or partly open beta-barrel with Greek key topology [ PUBMED:8475069 ].

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 Tudor (CL0049), which has the following description:

This clan covers the Tudor domain 'royal family' [1]. This includes chromo, MBT, PWWP and tudor domains. The chromo domain is a comprised of approximately 50 amino acid residues. There are usually one to three Chromo domains found in a single protein. In some chromo domain containing proteins, a second related chromo domain has been found and is referred to as the Chromo-shadow domain. The structure of the Chromo and Chromo-shadow domains reveal an OB-fold, a fold found in a variety of prokaryotic and eukaryotic nucleic acid binding proteins. More specifically,the chromo-domain structure reveals a three beta strands that are packed against an alpha helix. Interestingly, a similar structure is found in the archaeal chromatin proteins (7kDa DNA-binding domain). These are sequence neutral DNA binding proteins. The DNA binding in these archaeal proteins is mediated through the triple stranded beta sheet. These archaeal domains are though to represent an ancestral chromo domain. Homologs of the chromo domain have been found in fission yeast, ciliated protozoa and all animal species, but appear to be absent in eubacteria, budding yeast and plants [2]. The precise function of the chromo domain is unclear, but the chromo domain is thought to act as a targeting module for chromosomal proteins, although the chromosomal contexts and functional contexts being targeted vary. In all cases studies, the chromo domains are found in proteins that are involved in transcription regulation, positive and negative [2].

The clan contains the following 33 members:

53-BP1_Tudor 7kD_DNA_binding Agenet Chromo Chromo_2 Chromo_shadow Cul7 DUF1325 DUF4537 DUF4819 GEN1_C Hva1_TUDOR LBR_tudor LytTR MBT Mtf2_C ProQ_C PWWP Rad9_Rad53_bind RBB1NT SAWADEE SMN SNase TTD TUDOR Tudor-knot Tudor_1_RapA Tudor_2 Tudor_3 Tudor_4 Tudor_5 Tudor_FRX1 Tudor_RapA

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
(18)
Full
(14812)
Representative proteomes UniProt
(44465)
RP15
(2635)
RP35
(6739)
RP55
(12834)
RP75
(19363)
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
(18)
Full
(14812)
Representative proteomes UniProt
(44465)
RP15
(2635)
RP35
(6739)
RP55
(12834)
RP75
(19363)
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
(18)
Full
(14812)
Representative proteomes UniProt
(44465)
RP15
(2635)
RP35
(6739)
RP55
(12834)
RP75
(19363)
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: Alignment kindly provided by SMART
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: SMART
Number in seed: 18
Number in full: 14812
Average length of the domain: 107.7 aa
Average identity of full alignment: 22 %
Average coverage of the sequence by the domain: 45.09 %

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 21.0 21.0
Trusted cut-off 21.0 21.0
Noise cut-off 20.9 20.9
Model length: 108
Family (HMM) version: 20
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 SNase domain has been found. There are 349 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
A0A044R3I2 View 3D Structure Click here
A0A067CMC7 View 3D Structure Click here
A0A077ZC78 View 3D Structure Click here
A0A077ZG94 View 3D Structure Click here
A0A0D2GAJ7 View 3D Structure Click here
A0A0D2GXT3 View 3D Structure Click here
A0A0H3GWM0 View 3D Structure Click here
A0A0K0EGL8 View 3D Structure Click here
A0A0N4UDA6 View 3D Structure Click here
A0A0P0UYP3 View 3D Structure Click here
A0A175VX81 View 3D Structure Click here
A0A175W3L7 View 3D Structure Click here
A0A1C1CK95 View 3D Structure Click here
A0A1C1D2N1 View 3D Structure Click here
A0A1D6H9E9 View 3D Structure Click here
A0A1D6MKT1 View 3D Structure Click here
A0A1D8PTZ1 View 3D Structure Click here
A0A5K4F177 View 3D Structure Click here
A0A5K4F452 View 3D Structure Click here
A0A5S6PJP3 View 3D Structure Click here
A1CRW4 View 3D Structure Click here
A1D4S1 View 3D Structure Click here
A2Q8K8 View 3D Structure Click here
A3GI61 View 3D Structure Click here
A4HT00 View 3D Structure Click here
A4I7R1 View 3D Structure Click here
A4RMK0 View 3D Structure Click here
A5DNZ8 View 3D Structure Click here
A5E1Q5 View 3D Structure Click here
A7ECE0 View 3D Structure Click here
A7TE94 View 3D Structure Click here
B0D7T0 View 3D Structure Click here
B2AU25 View 3D Structure Click here
B2WC78 View 3D Structure Click here
B6H1W0 View 3D Structure Click here
B6JYT1 View 3D Structure Click here
B6QNP4 View 3D Structure Click here
B8JLW4 View 3D Structure Click here
B8MY73 View 3D Structure Click here
C0NC47 View 3D Structure Click here