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1  structure 360  species 0  interactions 645  sequences 7  architectures

Family: S1-P1_nuclease (PF02265)

Summary: S1/P1 Nuclease

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This is the Wikipedia entry entitled "S1 P1 nuclease protein domain". More...

S1 P1 nuclease protein domain Edit Wikipedia article

S1-P1 nuclease
PDB 1ak0 EBI.jpg
P1 nuclease in complex with a substrate analog
Identifiers
Symbol S1-P1_nuclease
Pfam PF02265
Pfam clan CL0368
InterPro IPR003154
SCOP 1ak0
SUPERFAMILY 1ak0

In molecular biology, S1 P1 nuclease refers to a protein domain with enzyme activity.This family contains both S1 and P1 nucleases (EC) which cleave RNA and single stranded DNA with no sequence specificity. They are found in both prokaryotes and eukaryotes and are thought to be associated in programmed cell death and also in tissue differentiation. Furthermore, they are secreted extracellular, that is, outside of the cell. Their function and distinguishing features mean they have potential in being exploited in the field of biotechnology.[1]

Function[edit]

The function of the P1/S1 nuclease, is to digest single-stranded (ss)RNA and DNA. It is a 36 kDa glycoprotein with very distinguishing features, they are:

These requirements and distinguishing features are responsible for function efficacy. It is an enzyme and these four features are needed for enzyme functionality. The three zinc ions are vital for catalysis. The first two zincs activate the attacking water in hydrolysis whilst the third zinc ion stabilizes the leaving oxyanion.[2][3]

Mechanism[edit]

This zinc-dependent nuclease protein domain produces 5' nucleotides and cleaves phosphate groups from 3' nucleotides. Additionally, the side chain of tryptophan located in the cavity in the active site and its backbone supports the action one of the zinc ions. Such mechanisms are essential to the catalytic function of the enzyme.[1]

References[edit]

  1. ^ a b Balabanova LA, Gafurov YM, Pivkin MV, Terentyeva NA, Likhatskaya GN, Rasskazov VA (2012). "An extracellular S1-type nuclease of marine fungus Penicillium melinii.". Mar Biotechnol (NY) 14 (1): 87–95. doi:10.1007/s10126-011-9392-5. PMID 21647618. 
  2. ^ Podzimek T, Matoušek J, Lipovová P, Poučková P, Spiwok V, Santrůček J (2011). "Biochemical properties of three plant nucleases with anticancer potential.". Plant Sci 180 (2): 343–51. doi:10.1016/j.plantsci.2010.10.006. PMID 21421379. 
  3. ^ Romier C, Dominguez R, Lahm A, Dahl O, Suck D (1998). "Recognition of single-stranded DNA by nuclease P1: high resolution crystal structures of complexes with substrate analogs.". Proteins 32 (4): 414–24. PMID 9726413. 

This article incorporates text from the public domain Pfam and InterPro IPR003154

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.

S1/P1 Nuclease Provide feedback

This family contains both S1 and P1 nucleases ( EC:3.1.30.1) which cleave RNA and single stranded DNA with no base specificity.

Literature references

  1. Romier C, Dominguez R, Lahm A, Dahl O, Suck D; , Proteins 1998;32:414-424.: Recognition of single-stranded DNA by nuclease P1: high resolution crystal structures of complexes with substrate analogs. PUBMED:9726413 EPMC:9726413


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR003154

This family contains both S1 and P1 nucleases (EC) which cleave RNA and single stranded DNA with no base specificity.

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 PhosC-NucP1 (CL0368), which has the following description:

This superfamily includes the Phospholipase C and P1-nuclease families.

The clan contains the following 5 members:

DUF2227 DUF4184 DUF457 S1-P1_nuclease Zn_dep_PLPC

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
(81)
Full
(645)
Representative proteomes NCBI
(699)
Meta
(285)
RP15
(171)
RP35
(268)
RP55
(338)
RP75
(375)
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Format an alignment

  Seed
(81)
Full
(645)
Representative proteomes NCBI
(699)
Meta
(285)
RP15
(171)
RP35
(268)
RP55
(338)
RP75
(375)
Alignment:
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Sequence:
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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
(81)
Full
(645)
Representative proteomes NCBI
(699)
Meta
(285)
RP15
(171)
RP35
(268)
RP55
(338)
RP75
(375)
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: Pfam-B_2480 (release 5.2)
Previous IDs: Nuclease;
Type: Domain
Author: Bateman A, Mian N
Number in seed: 81
Number in full: 645
Average length of the domain: 243.10 aa
Average identity of full alignment: 24 %
Average coverage of the sequence by the domain: 82.02 %

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 21.9 21.9
Trusted cut-off 21.9 22.0
Noise cut-off 21.8 21.7
Model length: 252
Family (HMM) version: 11
Download: download the raw HMM for this family

Species distribution

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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 S1-P1_nuclease domain has been found. There are 1 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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