Staphylococcal nuclease

From Proteopedia

Revision as of 08:42, 11 May 2014

Micrococcal nuclease structure

Micrococcal nuclease, or Staphylococcal nuclease, is a monomeric Ca++ dependent enzyme of 149 amino acids that cleaves either DNA or RNA substrates. It is used for relatively non-specific cleavage of nucleic acids in molecular biology, and has been an important model system for the study of protein folding.

Structure

The first structure was solved in 1969 in the Cotton lab at MIT, published in 1971^[1], and deposited in the PDB as now-obsoleted 1sns in April 1974. The highest resolution wildtype structure in the PDB with deposited data is 2snc at 1.65A[1]. As seen in the ribbon diagram above, the nuclease molecule has 3 long alpha helices and a 5-stranded, barrel-shaped beta sheet, in an arrangement known as the OB-fold (for oligonucleotide-binding fold) as classified in the SCOP database. There are about 200 PDB entries for Staph. nuclease, including extremely extensive mutational studies from many labs focused on understanding aspects of protein folding^[2][3][4].

3D structures of Staphylococcal nuclease

Updated on 11-May-2014

1sno, 1ey0, 1kaa, 1kab, 1kda, 1kdb, 1kdc, 1stg, 1sth, 1stn, 1syb, 1syc, 1syd, 1sye, 1syf, 1syg – SCN – Staphylococcus aureus
1tr5, 1u9r, 2pw5, 2pyk, 2pzw – SCN (mutant) – Room temperature 3sk4, 3sk5, 3sk6, 3sk8, 3sxh, 3t13, 3hej, 3hzx, 3nhh, 3itp, 3p75, 3lx0, 3meh, 3mvv, 3qoj, 3qol, 3qon, 3mhb, 3mxp, 3mz5, 3r3o, 3ruz, 3t16, 3tme, 3tp5, 3tp6, 3tp7, 3tp8, 3v2t, 3qb3, 3va5, 4df7, 4dfa, 4dgz, 4du9, 4e6i, 4eoa, 4eqn, 4eqo, 4eqp, 4evo, 4f7x, 4f8m, 2pw7, 2pzt, 2pzu, 2rdf, 2qdb, 2rbm, 3bdc, 3c1e, 3c1f, 3d4d, 3d6c, 3dmu, 3e5s, 3eji, 3ero, 3erq, 3d4w, 3d8g, 3dhq, 3h6m, 2f0e, 2f0f, 2f0g, 2f0h, 2f0i, 2f0j, 2f0k, 2f0l, 2f0m, 2f0n, 2f0o, 2f0p, 2f0q, 2f0s, 2f0t, 2f0u, 2f0v, 2f0w, 2oxp, 2oeo, 2of1, 2rks, 1snp, 1snq, 1joo, 1jor, 1tqo, 1tt2, 2exz, 2ey1, 2ey2, 2ey5, 2ey6, 2eyf, 2eyh, 2eyj, 2eyl, 2eym, 2eyo, 2eyp, 2f0d, 4ky7, 4ky6, 4ky5, 4kv6, 4kta, 4kjo, 4khv, 4kjn, 4kd4, 4kd3, 4k8j, 4k8i, 4k6d, 4k5x, 4k5w, 4k5v, 4k2l, 4k2k, 4k14, 4i65, 4j6h, 4id6, 4j1m, 4iz8, 4iun, 4ial, 4hth, 4hmj, 4hmi, 4h7b, 4g57, 1ena, 1ey4, 1ey6, 1ey7, 1ey8, 1ey9, 1eya, 1eyc, 1eyd, 1ez6, 1ez8, 1f2m, 1f2y, 1f2z, 1ihz, 1ii3, 1nuc, 1sta, 1stb, 1sty, 2snm, 3evq, 3shl, 3u9o, 4laa, 4me5, 4n9p, 4n9t, 4ndx, 4nkl, 4nmz, 4np5, 4odg – SCN (mutant) – Low temperature
2khs – SCN - NMR
2f3v, 1rkn – SCN residues 1-110 (mutant) – NMR
2pqe, 2m00, 2lkv – SCN residues 80-228 (mutant) – NMR
2f3w – SCN residues 1-110 – NMR
2sob - SCN residues 83-185 – NMR
1jok, 1joq, 3s9w, 3sr1 - SCN (mutant) + Ca + TBP
1a2t – SCN (mutant) + mercaptoethanol
1enc, 2enb – SCN + thymidine diphosphate
1a2u, 1snd, 2nuc – SCN (mutant) + thymidine diphosphate
1a3t – SCN (mutant) + thymidine diphosphate + fluoroethane thiol
1a3u, 1a3v – SCN (mutant) + cyclic thiol
1aex, 3nuc, 5nuc – SCN (mutant) + alkane thiol
1nsn – SCN + antibody

References

1. ↑ Arnone AA, Bier CJ, Cotton FA, Day VW, Hazen EE Jr, Richardson DC, Richardson JS, Yonath A (1971) "A High Resolution Structure of an Inhibitor Complex of the Extracellular Nuclease of Staphylococcus aureus: I. Experimental Procedures and Chain Tracing," J. Biol. Chem. 246, 2303-2316
2. ↑ Roche J, Caro JA, Norberto DR, Barthe P, Roumestand C, Schlessman JL, Garcia AE, Garcia-Moreno E B, Royer CA. Cavities determine the pressure unfolding of proteins. Proc Natl Acad Sci U S A. 2012 Apr 10. PMID:22496593 doi:10.1073/pnas.1200915109
3. ↑ Chen J, Lu Z, Sakon J, Stites WE. Proteins with simplified hydrophobic cores compared to other packing mutants. Biophys Chem. 2004 Aug 1;110(3):239-48. PMID:15228960 doi:10.1016/j.bpc.2004.02.007
4. ↑ Wynn R, Harkins PC, Richards FM, Fox RO. Mobile unnatural amino acid side chains in the core of staphylococcal nuclease. Protein Sci. 1996 Jun;5(6):1026-31. PMID:8762134 doi:http://dx.doi.org/10.1002/pro.5560050605