DB code: S00429

RLCP classification 1.15.11200.472 : Hydrolysis
CATH domain 3.60.10.10 : Deoxyribonuclease I; Chain A Catalytic domain
E.C. 3.1.21.1
CSA 1dnk
M-CSA 1dnk
MACiE M0041

CATH domain Related DB codes (homologues)
3.60.10.10 : Deoxyribonuclease I; Chain A S00428 S00430

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
P00639 Deoxyribonuclease-1
EC 3.1.21.1
Deoxyribonuclease I
DNase I
NP_776959.1 (Protein)
NM_174534.2 (DNA/RNA sequence)
PF03372 (Exo_endo_phos)
[Graphical View]

KEGG enzyme name
deoxyribonuclease 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

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P00639 DNAS1_BOVIN Endonucleolytic cleavage to 5''- phosphodinucleotide and 5''-phosphooligonucleotide end-products. Secreted. Nucleus envelope. Note=Secretory protein, stored in zymogen granules and found in the nuclear envelope. Divalent cations. Prefers calcium or magnesium.

KEGG Pathways
Map code Pathways E.C.

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00305 C00076 C00001 C00039 C00434 C03236 C00351
E.C.
Compound Magnesium Calcium H2O DNA Double-stranded DNA 5'-Phosphodinucleotide 5'-Phosphooligonucleotide
Type divalent metal (Ca2+, Mg2+) divalent metal (Ca2+, Mg2+) H2O nucleic acids nucleic acids nucleic acids,phosphate group/phosphate ion nucleic acids,phosphate group/phosphate ion
ChEBI 18420
 18420
 		29108
 29108
 		15377
 15377
PubChem 888
 888
 		271
 271
 		22247451
 962
 22247451
 962
1atnD Bound:3x_CA Unbound Unbound Unbound Unbound Unbound
1dnkA Unbound Unbound Unbound Bound:G-G-T-A-T-A-C (chain C:double stranded DNA) Unbound Unbound
2dnjA Unbound Unbound Unbound Unbound Unbound Bound:G-C-G-A-T-C (chain C:double stranded DNA)
3dniA Bound:2x_CA Unbound Unbound Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1atnD GLU 78;HIS 134;ASP 212;HIS 252 GLU 39;ASP 168;ASP 251(divalent metal)
1dnkA GLU 78;HIS 134;ASP 212;HIS 252 GLU 39;ASP 168;ASP 251(divalent metal)
2dnjA GLU 78;HIS 134;ASP 212;HIS 252 GLU 39;ASP 168;ASP 251(divalent metal)
3dniA GLU 78;HIS 134;ASP 212;HIS 252 GLU 39;ASP 168;ASP 251(divalent metal)

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[4]
p.1253-1254, Fig.16 2
[5]
p.629-631

References
[1]
Resource
Comments X-ray crystallography (2 Angstroms)
Medline ID
PubMed ID 3560229
Journal J Mol Biol
Year 1986
Volume 192
Pages 605-632
Authors Oefner C, Suck D
Title Crystallographic refinement and structure of DNase I at 2 A resolution.
Related PDB 3dni
Related UniProtKB
[2]
Resource
Comments X-ray crystallography (2.8/3.0 Angstroms)
Medline ID
PubMed ID 2395459
Journal Nature
Year 1990
Volume 347
Pages 37-44
Authors Kabsch W, Mannherz HG, Suck D, Pai EF, Holmes KC
Title Atomic structure of the actin:DNase I complex.
Related PDB 1atn
Related UniProtKB P02568
[3]
Resource
Comments X-ray crystallography (2 Angstroms)
Medline ID
PubMed ID 1748997
Journal J Mol Biol
Year 1991
Volume 222
Pages 645-667
Authors Lahm A, Suck D
Title DNase I-induced DNA conformation. 2 A structure of a DNase I-octamer complex.
Related PDB 2dnj
Related UniProtKB
[4]
Resource
Comments X-ray crystallography (2.3 Angstroms)
Medline ID
PubMed ID 1518054
Journal J Mol Biol
Year 1992
Volume 226
Pages 1237-1256
Authors Weston SA, Lahm A, Suck D
Title X-ray structure of the DNase I-d(GGTATACC)2 complex at 2.3 A resolution.
Related PDB 1dnk
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 9057832
Journal Eur J Biochem
Year 1997
Volume 243
Pages 684-9
Authors Black CB, Cowan JA
Title Inert 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.
Related PDB
Related UniProtKB

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.

Created Updated
2002-07-01 2009-02-26