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), metal ion binding (GO:0046872), hydrolase activity (GO:0016787)

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

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

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

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	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