| SMART accession number: | SM00892
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| 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. |
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| 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.
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| GO function: | hydrolase activity (GO:0016787), metal ion binding (GO:0046872), nucleic acid binding (GO:0003676) |
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| Family alignment: |
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Click on the following links for more information.
- Evolution (species in which this domain is found)
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- Cellular role (predicted cellular role)
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Cellular role: chromatin
- Literature (relevant references for this domain)
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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 |
| 3ism |  | Crystal structure of the endog/endogi complex: mechanism of endog inhibition |
- Links (links to other resources describing this domain)
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