SMART: Endonuclease_NS domain annotation

Endonuclease_NS DNA/RNA non-specific endonuclease

SMART accession number:	SM00892
Description:	A family of bacterial and eukaryotic endonucleases 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. An 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.
Interpro abstract (IPR001604):	A 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 [ (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.
GO function:	nucleic acid binding (GO:0003676), hydrolase activity (GO:0016787), metal ion binding (GO:0046872)
Family alignment:	View or

There are 13023 Endonuclease_NS domains in 12891 proteins in SMART's nrdb database.

Click on the following links for more information.

Evolution (species in which this domain is found)
Taxonomic distribution of proteins containing Endonuclease_NS domain.
This tree includes only several representative species. The complete taxonomic breakdown of all proteins with Endonuclease_NS domain is also avaliable.

Click on the protein counts, or double click on taxonomic names to display all proteins containing Endonuclease_NS domain in the selected taxonomic class.
Cellular role (predicted cellular role)
Cellular role: chromatin
Literature (relevant references for this domain)
Primary literature is listed below; Automatically-derived, secondary literature is also avaliable.
- Friedhoff P, Gimadutdinow O, Pingoud A
- Identification of catalytically relevant amino acids of the extracellularSerratia marcescens endonuclease by alignment-guided mutagenesis.
- Nucleic Acids Res. 1994; 22: 3280-7
- Display abstract
- By sequence alignment of the extracellular Serratia marcescens nucleasewith three related nucleases we have identified seven charged amino acidresidues which are conserved in all four sequences. Six of these residuestogether with four other partially conserved His or Asp residues werechanged to alanine by site-directed PCR-mediated mutagenesis using avariant of the nuclease gene in which the coding sequence of the signalpeptide was replaced by the coding sequence for an N-terminal affinity tag[Met(His)6GlySer]. Four of the mutant proteins showed almost no reductionin nuclease activity but five displayed a 10- to 1000-fold reduction inactivity and one (His110Ala) was inactive. Based upon these results it issuggested that the S.marcescens nuclease employs a mechanism in whichHis110 acts in concert with a Mg2+ ion and three carboxylates (Asp107,Glu148 and Glu232) as well as one or two basic amino acid residues(Arg108, Arg152).
- Miller MD, Tanner J, Alpaugh M, Benedik MJ, Krause KL
- 2.1 A structure of Serratia endonuclease suggests a mechanism for bindingto double-stranded DNA.
- Nat Struct Biol. 1994; 1: 461-8
- Display abstract
- The crystal structure of Serratia endonuclease has been solved to 2.1 A bymultiple isomorphous replacement. This magnesium-dependent enzyme isequally active against single- and double-stranded DNA, as well as RNA,without any apparent base preference. The Serratia endonuclease fold isdistinct from that of other nucleases that have been solved by X-raydiffraction. The refined structure consists of a central layer containingsix antiparallel beta-strands which is flanked on one side by a helicaldomain and on the opposite side by one dominant helix and a very longcoiled loop. Electrostatic calculations reveal a strongly polarizedmolecular surface and suggest that a cleft between this long helix andloop, near His 89, may contain the active site of the enzyme.
Structure (3D structures containing this domain)

3D Structures of Endonuclease_NS domains in PDB

PDB code	Main view	Title
1g8t		SM ENDONUCLEASE FROM SERATIA MARCENSCENS AT 1.1 A RESOLUTION
1qae		THE ACTIVE SITE OF SERRATIA ENDONUCLEASE CONTAINS A CONSERVED MAGNESIUM-WATER CLUSTER
1ql0		Sm Endonuclease from Seratia marcenscens at atomic resolution
1smn		IDENTIFICATION OF THE SERRATIA ENDONUCLEASE DIMER: STRUCTURAL BASIS AND IMPLICATIONS FOR CATALYSIS
1zm8		Apo Crystal structure of Nuclease A from Anabaena sp.
2o3b		Crystal structure complex of Nuclease A (NucA) with intra-cellular inhibitor NuiA
2xgr		extracellular endonuclease
2xh3		extracellular nuclease
2xr9		Crystal structure of Autotaxin (ENPP2)
2xrg		Crystal structure of Autotaxin (ENPP2) in complex with the HA155 boronic acid inhibitor
3ism		Crystal structure of the EndoG/EndoGI complex: Mechanism of EndoG inhibition
3nkm		Crystal structure of mouse autotaxin
3nkn		Crystal structure of mouse autotaxin in complex with 14:0-LPA
3nko		Crystal structure of mouse autotaxin in complex with 16:0-LPA
3nkp		Crystal structure of mouse autotaxin in complex with 18:1-LPA
3nkq		Crystal structure of mouse autotaxin in complex with 18:3-LPA
3nkr		Crystal structure of mouse autotaxin in complex with 22:6-LPA
3owv		Structural insights into catalytic and substrate binding mechanisms of the strategic EndA nuclease from Streptococcus pneumoniae
3s5b		Crystal Structure of CED-3 Protease Suppressor-6 (CPS-6) from Caenorhabditis elegans
3wav		Crystal Structure of Autotaxin in Complex with Compound 10
3waw		Crystal Structure of Autotaxin in Complex with 2BoA
3wax		Crystal Structure of Autotaxin in Complex with 3BoA
3way		Crystal Structure of Autotaxin in Complex with 4BoA
4a1n		Human Mitochondrial endo-exonuclease
4b56		Structure of ectonucleotide pyrophosphatase-phosphodiesterase-1 (NPP1)
4e3y		X-ray structure of the Serratia marcescens endonuclease at 0.95 A resolution
4gtw		Crystal structure of mouse Enpp1 in complex with AMP
4gtx		Crystal structure of mouse Enpp1 in complex with TMP
4gty		Crystal structure of mouse Enpp1 in complex with GMP
4gtz		Crystal structure of mouse Enpp1 in complex with CMP
4qgo		4QGO
4qh0		4QH0
4qn0		4QN0
4zg6		4ZG6
4zg7		4ZG7
4zg9		4ZG9
4zga		4ZGA
5dlt		5DLT
5dlv		5DLV
5dlw		5DLW
5fgu		5FGU
5fgw		5FGW
5gkc		5GKC
5gkp		5GKP
5hrt		5HRT
5ijq		5IJQ
5ijs		5IJS
5kxa		5KXA
5l0b		5L0B
5l0e		5L0E
5l0k		5L0K
5lia		5LIA

Links (links to other resources describing this domain)
PFAM Endonuclease_NS
INTERPRO IPR001604

Endonuclease_NS

Taxonomic distribution of proteins containing Endonuclease_NS domain.

3D Structures of Endonuclease_NS domains in PDB