EzCatDB: S00022

DB codeS00022
RLCP classification1.15.8240.2170
CATH domainDomain 11.10.575.10Catalytic domain
E.C.3.1.30.1
CSA1ak0


Enzyme Name
Swiss-protKEGG

P24289
Protein nameNuclease P1Aspergillus nuclease S1
endonuclease S1 (Aspergillus)
single-stranded-nucleate endonuclease
deoxyribonuclease S1
deoxyribonuclease S1
nuclease S1
Neurospora crassa single-strand specific endonuclease
S1 nuclease
single-strand endodeoxyribonuclease
single-stranded DNA specific endonuclease
single-strand-specific endodeoxyribonuclease
single strand-specific DNase
Aspergillus oryzae S1 nuclease
SynonymsEC 3.1.30.1
Endonuclease P1
Deoxyribonuclease P1


Swiss-prot:Accession NumberP24289
Entry nameNUP1_PENCI
ActivityEndonucleolytic cleavage to 5''- phosphomononucleotide and 5''-phosphooligonucleotide end-products.
Subunit
Subcellular locationSecreted.
CofactorBinds 3 zinc ions.


CofactorsSubstratesProducts
KEGG-idC00038C00046C00039C00001C00171C00351
CompoundZincRNADNAH2O5'-Phosphomononucleotide5'-Phosphooligonucleotide
Typeheavy metalnucleic acidsnucleic acidsH2Onucleotidenucleic acids,phosphate group/phosphate ion
1ak0ABound:3x_ZNUnboundUnbound
Analogue:ADS-THS-THS-THSUnbound

Active-site residues
resource
Swiss-prot;P24289 & literature [2]
pdbCatalytic residuesCofactor-binding residues
1ak0AASP 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
ReferencesSectionsNo. of steps in catalysis
[1]p.1615-1616
[2]p.421-423, Fig.6

references
[1]
CommentsX-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS).
PubMed ID1710977
JournalEMBO J
Year1991
Volume10
Pages1607-18
AuthorsVolbeda A, Lahm A, Sakiyama F, Suck D
TitleCrystal structure of Penicillium citrinum P1 nuclease at 2.8 A resolution.
Related Swiss-protP24289
[2]
CommentsX-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS).
PubMed ID9726413
JournalProteins
Year1998
Volume32
Pages414-24
AuthorsRomier C, Dominguez R, Lahm A, Dahl O, Suck D
TitleRecognition of single-stranded DNA by nuclease P1: high resolution crystal structures of complexes with substrate analogs.
Related PDB1ak0
Related Swiss-protP24289
[3]
PubMed ID10563833
JournalChem Res Toxicol
Year1999
Volume12
Pages1077-82
AuthorsWang Y, Taylor JS, Gross ML
TitleNuclease 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.

createdupdated
2004-03-192009-03-11


Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2010)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)

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