|
|
| Enzyme Name | | Swiss-prot | KEGG |
|---|
| P24289 |
|---|
| Protein name | Nuclease P1 | Aspergillus nuclease S1endonuclease S1 (Aspergillus)single-stranded-nucleate endonucleasedeoxyribonuclease S1deoxyribonuclease S1nuclease S1Neurospora crassa single-strand specific endonucleaseS1 nucleasesingle-strand endodeoxyribonucleasesingle-stranded DNA specific endonucleasesingle-strand-specific endodeoxyribonucleasesingle strand-specific DNaseAspergillus oryzae S1 nuclease |
|---|
| Synonyms | EC 3.1.30.1Endonuclease P1Deoxyribonuclease P1 |
|---|
| Swiss-prot:Accession Number | P24289 |
|---|
| Entry name | NUP1_PENCI |
|---|
| Activity | Endonucleolytic cleavage to 5''- phosphomononucleotide and 5''-phosphooligonucleotide end-products. |
|---|
| Subunit |
|
|---|
| Subcellular location | Secreted. |
|---|
| Cofactor | Binds 3 zinc ions. |
|---|
| Cofactors | Substrates | Products |
|---|
| KEGG-id | C00038 | C00046 | C00039 | C00001 | C00171 | C00351 |
|---|
| Compound | Zinc | RNA | DNA | H2O | 5'-Phosphomononucleotide | 5'-Phosphooligonucleotide |
|---|
| Type | heavy metal | nucleic acids | nucleic acids | H2O | nucleotide | nucleic acids,phosphate group/phosphate ion |
|---|
| 1ak0A |  | Bound:3x_ZN | Unbound | Unbound |
| Analogue:ADS-THS-THS-THS | Unbound |
|---|
| Active-site residues | | resource |
|---|
| Swiss-prot;P24289 & literature [2] | | pdb | Catalytic residues | Cofactor-binding residues |
|---|
| 1ak0A | | ASP 45;ARG 48
| TRP 1;HIS 6(Zinc3 binding);ASP 45;HIS 60;HIS 116(Zinc1 binding);ASP 120(Zinc1 & Zinc2 binding);HIS 126;HIS 149;ASP 153(Zinc2 binding)
|
|---|
| References for Catalytic Mechanism | | References | Sections | No. of steps in catalysis |
|---|
| [1] | p.1615-1616 |
| | [2] | p.421-423, Fig.6 |
|
| references | | [1] |
|---|
| Comments | X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS). |
|---|
| PubMed ID | 1710977 |
|---|
| Journal | EMBO J |
|---|
| Year | 1991 |
|---|
| Volume | 10 |
|---|
| Pages | 1607-18 |
|---|
| Authors | Volbeda A, Lahm A, Sakiyama F, Suck D |
|---|
| Title | Crystal structure of Penicillium citrinum P1 nuclease at 2.8 A resolution. |
|---|
| Related Swiss-prot | P24289 |
|---|
| [2] |
|---|
| Comments | X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS). |
|---|
| PubMed ID | 9726413 |
|---|
| Journal | Proteins |
|---|
| Year | 1998 |
|---|
| Volume | 32 |
|---|
| Pages | 414-24 |
|---|
| Authors | Romier C, Dominguez R, Lahm A, Dahl O, Suck D |
|---|
| Title | Recognition of single-stranded DNA by nuclease P1: high resolution crystal structures of complexes with substrate analogs. |
|---|
| Related PDB | 1ak0 |
|---|
| Related Swiss-prot | P24289 |
|---|
| [3] |
|---|
| PubMed ID | 10563833 |
|---|
| Journal | Chem Res Toxicol |
|---|
| Year | 1999 |
|---|
| Volume | 12 |
|---|
| Pages | 1077-82 |
|---|
| Authors | Wang Y, Taylor JS, Gross ML |
|---|
| Title | Nuclease P1 digestion combined with tandem mass spectrometry for the structure determination of DNA photoproducts. |
|---|
| comments | According to the literature [2], the hydrolytic reaction, where a water is activated by cofactor zinc ion, proceeds as follows:
(1) A water molecule, which is bridging cofactors, Zinc1 and Zinc3, is activated to make a hydroxide ion. This activation is assisted by Asp45, which is also ligating zinc1.
(2) The activated water makes a nucleophilic attack on the phosphorus atom of the scissile phosphoric ester bond, in line with the P-O3' bond. (This attack will lead to the inversion of the phosphate, suggsting an SN2-like reaction.)
(3) The pentacovalent transition state is stabilized by Zinc2 and Arg48.
(4) Finally, the P-O3' bond will be cleaved.
|
| created | updated |
|---|
| 2004-03-19 | 2009-03-11 |
|
|
