DNaseIc

deoxyribonuclease I

• SMART accession number: SM00476
• Description: Deoxyribonuclease I catalyzes the endonucleolytic cleavage of double-stranded DNA. The enzyme is secreted outside the cell and also involved in apoptosis in the nucleus.
• Interpro abstract (IPR008185):

  Deoxyribonuclease I (DNase I) (EC 3.1.21.1) [(PUBMED:3713845)] is a vertebrate enzyme which catalyzes the endonucleolytic cleavage of double-stranded DNA to 5'- phosphodinucleotide and 5'-phosphooligonucleotide end-products. DNase I is an enzyme involved in DNA degradation; it is normally secreted outside of the cell but seems to be able to gain access to the nucleus where it is involved in cell death by apoptosis [(PUBMED:8428592)].

  As shown in the following schematic representation, DNase I is a glycoprotein of about 260 residues with two conserved disulphide bonds.

                                +-+               +--------+
                                | |               |        |
        xxxxxxxxxxxxxxxxx#xxxxxxCxCxxxxx#xxxxxxxxxCxxxxxxxxCxxxxxxxxxxxxx
  'C': conserved cysteine involved in a disulphide bond.
  '#': active site residue.
  

  DNase I has a pH-optimum around 7.5 and requires calcium and magnesium for full activity. It causes single strand nicks in duplex DNA. A proton acceptor-donor chain composed of an histidine and a glutamic acid produce a nucleophilic hydroxyl ion from water, which cleaves the 3'-P-O bond [(PUBMED:3352748)].

  DNase I forms a 1:1 complex with G-actin, resulting in the inhibition of DNase activity and loss of the ability of G-actin to polymerise into fibres [(PUBMED:2395459)].

  DNase I has been used in the treatment of lung problems in patients with cystic fibrosis: here it acts by degrading DNA found in purulent lung secretions, reducing their viscosity and making it easier for the patient to breathe [(PUBMED:2251263)].

  The sequence of DNase I is evolutionary related to that of human muscle-specific DNase-like protein and human proteins DHP1 and DHP2. However, the first disulphide bond of DNase I is not conserved in these proteins.

• GO process: DNA catabolic process (GO:0006308)
• GO function: deoxyribonuclease activity (GO:0004536)

There are 247 DNaseIc domains in 241 proteins in SMART's nrdb database.

Literature (relevant references for this domain)

Primary literature is listed below; Automatically-derived, secondary literature is also avaliable.

• Blumenthal SS, Ren L, Lewand DL, Krezoski SK, Petering DH
• Cadmium decreases SGLT1 messenger RNA in mouse kidney cells.
• Toxicol Appl Pharmacol. 1998; 149: 49-54

Mouse renal cortical tubule cells in primary culture exposed to cadmium (Cd2+) develop decreased Na(+)-glucose cotransport activity as measured by uptake of the glucose analogue alpha-methyl-glucoside. RNA was isolated from kidney cell cultures, and after reversed transcription, the DNA was amplified with primers to rat SGLT1 (the high affinity isoform of the sodium glucose cotransporter) and mouse beta-actin. Only one product was identified after amplification with the rat SGLT1 primers, which on sequencing was 96% identical to rat SGLT1. Compared to beta-actin, the intensity of the SGLT1 message declined progressively as CdCl2 concentration in the medium increased from 0 to 10 microM. Similar decreases in SGLT1 mRNA were also observed as media zinc (Zn2+) concentrations rose from 0 to 75 microM or as copper (Cu) concentrations increased from 0 to 150 microM. Exposure to 8 microM Cd as Cd-metallothionein (Cd7-MT) also caused a fall in relative SGLT1 mRNA abundance, and at nearly identical internal Cd concentrations of 40-43 pmol/microgram DNA, both Cd7-MT and CdCl2 reduced SGLT1 mRNA to 33% of control. In general, the fall in SGLT1 mRNA was more rapid than the decline in Na(+)-dependent glucose uptake after cells were exposed to Cd2+. These findings suggest that the effects of Cd2+ and other metals on renal glucose transport are related to decreased expression of SGLT1 message.

• Suck D
• DNA recognition by DNase I.
• J Mol Recognit. 1994; 7: 65-70

Bovine pancreatic DNase I shows a strong preference for double-stranded substrates and cleaves DNA with strongly varying cutting rates suggesting that the enzyme recognises sequence-dependent structural variations of the DNA double helix. The complicated cleavage pattern indicates that several local as well as global helix parameters influence the cutting frequency of DNase I at a given bond. The high resolution crystal structures of two DNase I-DNA complexes showed that the enzyme binds tightly in the minor groove, and to the sugar-phosphate backbones of both strands, and thereby induces a widening of the minor groove and a bending towards the major groove. In agreement with biochemical data this suggests that flexibility and minor groove geometry are major parameters determining the cutting rate of DNase I. Experimental observations showing that the sequence environment of a dinucleotide step strongly affects its cleavage efficiency can be rationalized by the fact that six base pairs are in contact with the enzyme. Mutational analysis based on the structural results has identified critical residues for DNA binding and cleavage and has lead to a proposal for the catalytic mechanism.

• Lahm A, Suck D
• DNase I-induced DNA conformation. 2 A structure of a DNase I-octamer complex.
• J Mol Biol. 1991; 222: 645-67

The structure of a complex between DNase I and d(GCGATCGC)2 has been solved by molecular replacement and refined to an R-factor of 0.174 for all data between 6 and 2 A resolution. The nicked octamer duplexes have lost a dinucleotide from the 3' ends of one strand and are hydrogen-bonded across a 2-fold axis to form a quasi-continuous double helix of 14 base-pairs. DNase I is bound in the minor groove of the B-type DNA duplex forming contacts in and along both sides of the minor groove extending over a total of six base-pairs. As a consequence of binding of DNase I to the DNA-substrate the minor groove opens by about 3 A and the duplex bends towards the major groove by about 20 degrees. Apart from these more global distortions the bound duplex also shows significant deviations in local geometry. A major cause for the observed perturbations in the DNA conformation seems to be the stacking type interaction of a tyrosine ring (Y76) with a deoxyribose. In contrast, the enzyme structure is nearly unchanged compared to free DNase I (0.49 A root-mean-square deviations for main-chain atoms) thus providing a rigid framework to which the DNA substrate has to adapt on binding. These results confirm the hypothesis that groove width and stiffness are major factors determining the global sequence dependence of the enzyme's cutting rates. The nicked octamer present in the crystals did not allow us to draw detailed conclusions about the catalytic mechanism but confirmed the location of the active site near H134 on top of the central beta-sheets. A second cut of the DNA induced by diffusion of Mn2+ into the crystals may suggest the presence of a secondary active site in DNase I.

• Suck D, Oefner C
• Structure of DNase I at 2.0 A resolution suggests a mechanism for binding to and cutting DNA.
• Nature. 1986; 321: 620-5

Bovine pancreatic deoxyribonuclease I (DNase I), an endonuclease that degrades double-stranded DNA in a nonspecific but sequence-dependent manner, has been used as a biochemical tool in various reactions, in particular as a probe for the structure of chromatin and for the helical periodicity of DNA on the nucleosome and in solution. Limited digestion by DNase I, termed DNase I 'footprinting', is routinely used to detect protected regions in DNA-protein complexes. Recently, we have solved the three-dimensional structure of this glycoprotein (relative molecular mass 30,400) by X-ray structure analysis at 2.5 A resolution and have subsequently refined it crystallographically at 2.0 A. Based on the refined structure and the binding of Ca2+-thymidine 3',5'-diphosphate (Ca-pTp) at the active site, we propose a mechanism of action and present a model for the interaction of DNase I with double-stranded DNA that involves the binding of an exposed loop region in the minor groove of B-DNA and electrostatic interactions of phosphates from both strands with arginine and lysine residues on either side of this loop. We explain DNase I cleavage patterns in terms of this model and discuss the consequences of the extended DNase I-DNA contact region for the interpretation of DNase I footprinting results.

Disease (disease genes where sequence variants are found in this domain)

SwissProt sequences and OMIM curated human diseases associated with missense mutations within the DNaseIc domain.

Protein	Disease
Deoxyribonuclease-1 (P24855) (SMART)	OMIM:125505: DEOXYRIBONUCLEASE I; DNASE1

Structure (3D structures containing this domain)

3D Structures of DNaseIc domains in PDB

PDB code	Title
1atn	Atomic structure of the actin:dnase i complex
1dnk	The x-ray structure of the dnase i-d(ggtatacc)2 complex at 2.3 angstroms resolution
2a3z	Ternary complex of the wh2 domain of wasp with actin-dnase i
2a40	Ternary complex of the wh2 domain of wave with actin-dnase i
2a41	Ternary complex of the wh2 domain of wip with actin-dnase i
2a42	Actin-dnase i complex
2d1k	Ternary complex of the wh2 domain of mim with actin-dnase i
2dnj	Dnase i-induced dna conformation. 2 angstroms structure of a dnase i-octamer complex
3cjc	Actin dimer cross-linked by v. cholerae martx toxin and complexed with dnase i and gelsolin-segment 1
3dni	Crystallographic refinement and structure of dnase i at 2 angstroms resolution

Links (links to other resources describing this domain)

• INTERPRO: IPR008185
• PROSITE: DNASE_I_1