EzCatDB: S00429

DB codeS00429
RLCP classification1.15.11200.472
CATH domainDomain 13.60.10.10Catalytic domain
E.C.3.1.21.1
CSA1dnk
MACiEM0041

CATH domainRelated DB codes (homologues)
3.60.10.10S00428,S00430

Enzyme Name
Swiss-protKEGG

P00639
Protein nameDeoxyribonuclease-1deoxyribonuclease I
pancreatic DNase
DNase
thymonuclease, dornase
dornava
dornavac
pancreatic deoxyribonuclease
pancreatic dornase
deoxyribonuclease (pancreatic)
pancreatic DNase
DNAase
deoxyribonucleic phosphatase
DNase I
alkaline deoxyribonuclease
alkaline DNase
endodeoxyribonuclease I
DNA depolymerase
Escherichia coli endonuclease I
deoxyribonuclease A
DNA endonuclease
DNA nuclease
SynonymsEC 3.1.21.1
Deoxyribonuclease I
DNase I


Swiss-prot:Accession NumberP00639
Entry nameDNAS1_BOVIN
ActivityEndonucleolytic cleavage to 5''- phosphodinucleotide and 5''-phosphooligonucleotide end-products.
Subunit
Subcellular locationSecreted. Nucleus envelope. Note=Secretory protein, stored in zymogen granules and found in the nuclear envelope.
CofactorDivalent cations. Prefers calcium or magnesium.


CofactorsSubstratesProducts
KEGG-idC00305C00076C00039C00001C00434C03236C00351
CompoundMagnesiumCalciumDNAH2ODouble-stranded DNA5'-Phosphodinucleotide5'-Phosphooligonucleotide
Typedivalent metal (Ca2+, Mg2+)divalent metal (Ca2+, Mg2+)nucleic acidsH2Onucleic acidsnucleic acids,phosphate group/phosphate ionnucleic acids,phosphate group/phosphate ion
1atnDBound:3x_CAUnboundUnbound
UnboundUnboundUnbound
1dnkAUnboundUnboundUnbound
Bound:G-G-T-A-T-A-C(chain C:double stranded DNA)UnboundUnbound
2dnjAUnboundUnboundUnbound
UnboundUnboundBound:G-C-G-A-T-C(chain C:double stranded DNA)
3dniABound:2x_CAUnboundUnbound
UnboundUnboundUnbound

Active-site residues
pdbCatalytic residuesCofactor-binding residues
1atnDGLU 78;HIS 134;ASP 212;HIS 252
GLU 39;ASP 168;ASP 251(divalent metal)
1dnkAGLU 78;HIS 134;ASP 212;HIS 252
GLU 39;ASP 168;ASP 251(divalent metal)
2dnjAGLU 78;HIS 134;ASP 212;HIS 252
GLU 39;ASP 168;ASP 251(divalent metal)
3dniAGLU 78;HIS 134;ASP 212;HIS 252
GLU 39;ASP 168;ASP 251(divalent metal)

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[4]p.1253-1254, Fig.162
[5]p.629-631

references
[1]
CommentsX-ray crystallography (2 Angstroms)
PubMed ID3560229
JournalJ Mol Biol
Year1986
Volume192
Pages605-632
AuthorsOefner C, Suck D
TitleCrystallographic refinement and structure of DNase I at 2 A resolution.
Related PDB3dni
[2]
CommentsX-ray crystallography (2.8/3.0 Angstroms)
PubMed ID2395459
JournalNature
Year1990
Volume347
Pages37-44
AuthorsKabsch W, Mannherz HG, Suck D, Pai EF, Holmes KC
TitleAtomic structure of the actin:DNase I complex.
Related PDB1atn
Related Swiss-protP02568
[3]
CommentsX-ray crystallography (2 Angstroms)
PubMed ID1748997
JournalJ Mol Biol
Year1991
Volume222
Pages645-667
AuthorsLahm A, Suck D
TitleDNase I-induced DNA conformation. 2 A structure of a DNase I-octamer complex.
Related PDB2dnj
[4]
CommentsX-ray crystallography (2.3 Angstroms)
PubMed ID1518054
JournalJ Mol Biol
Year1992
Volume226
Pages1237-1256
AuthorsWeston SA, Lahm A, Suck D
TitleX-ray structure of the DNase I-d(GGTATACC)2 complex at 2.3 A resolution.
Related PDB1dnk
[5]
PubMed ID9057832
JournalEur J Biochem
Year1997
Volume243
Pages684-9
AuthorsBlack CB, Cowan JA
TitleInert chromium and cobalt complexes as probes of magnesium-dependent enzymes. Evaluation of the mechanistic role of the essential metal cofactor in Escherichia coli exonuclease III.

comments
This enzyme belongs to the DNase I family.
According to the literature [4], His252 acts as a general base, which abstracts a proton from the attacking water, whilst His314 serve as a general acid, protonating the leaving O3'.
Moreover, the paper [4] also mentioned the role of the divalent metal, which is supposed to be function as a cofactor. This metal ion, which is co-ordinated to the scissile phosphate group, Glu39, and possilbly Asp251, stabilizes the penta-covalent transition state and correctly positions the phosphate group relative to the active site.
The paper [5] supported the report by the paper [4], using mutagenesis technique.

createdupdated
2002-07-012009-02-26
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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