Summary: S1/P1 Nuclease
This is the Wikipedia entry entitled "S1 P1 nuclease protein domain". More...
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S1 P1 nuclease protein domain Edit Wikipedia article
P1 nuclease in complex with a substrate analog
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.
- a requirement for three zinc ions,
- containing common active site motifs and
- requires an acidic pH for catalysis.
- contains three glycans bound to the amino acid asparagine via N-glycosylation
- two Disulphide bridges between cysteine residues.
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.
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.
- 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.
- 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.
- 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. doi:10.1002/(sici)1097-0134(19980901)32:4<414::aid-prot2>3.0.co;2-g. PMID 9726413.
S1/P1 Nuclease Provide feedback
This family contains both S1 and P1 nucleases ( EC:22.214.171.124) which cleave RNA and single stranded DNA with no base specificity.
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
Internal database links
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR003154
This family summarizes both S1 and P1 nucleases (EC) which cleave RNA and single stranded DNA with no base specificity [PUBMED:12586391]. S1 nuclease is more active on DNA than RNA. Its reaction products are oligonucleotides or single nucleotides with 5' phosphoryl groups [PUBMED:6101052]. Although its primary substrate is single-stranded, it may also introduce single-stranded breaks in double-stranded DNA or RNA, or DNA-RNA hybrids. It is used as a reagent in nuclease protection assays and in removing single stranded tails from DNA molecules to create blunt ended molecules and opening hairpin loops generated during synthesis of double stranded cDNA. P1 nuclease cleaves its substrate at every position yielding nucleoside 5' monophosphates, and it does not recognize or act on double-stranded DNA [PUBMED:9726413]. It is useful at removing single stranded strands hanging off the end of double stranded DNA and at completely cleaving melted DNA for simple DNA composition analysis.
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||endonuclease activity (GO:0004519)|
|nucleic acid binding (GO:0003676)|
|Biological process||DNA catabolic process (GO:0006308)|
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
- the UniProt description of the protein sequence
- the number of residues in the sequence
- the Pfam graphic itself.
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We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the UniProtKB sequence database using the family HMM
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
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Curation and family details
|Seed source:||Pfam-B_2480 (release 5.2)|
|Author:||Bateman A, Mian N|
|Number in seed:||50|
|Number in full:||1659|
|Average length of the domain:||244.60 aa|
|Average identity of full alignment:||25 %|
|Average coverage of the sequence by the domain:||82.59 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 26740544 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||15|
|Download:||download the raw HMM for this family|
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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 12 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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