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Overview for MACiE Entry M0041

Version history

General Information

EC Number: 3.1.21.1 (A member of the Hydrolases, Acting on ester bonds, Endodeoxyribonucleases producing 5'-phosphomonoesters)

Enzyme Name: deoxyribonuclease I

Biological Species: Bos taurus (Cow)

Catalytic Chain UniprotKB Accession Codes:

Representative PDB Code: 1dnk - THE X-RAY STRUCTURE OF THE DNASE I-D(GGTATACC)2 COMPLEX AT 2.3ANGSTROMS RESOLUTION (Resolution = 2.30 Å).

Catalytic CATH Codes:

Display structure information

Overall Reaction:

Image of DNA

Image of water

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Image of DNA-5-phosphate

Image of DNA-3-hydroxyl

DNA
C00039
CHEBI:16991
water
C00001
CHEBI:15377
DNA-5-phosphate
X00015
DNA-3-hydroxyl
X00016

Overall Comment: Identity of the magnesium ions has been arbitrarily assigned due to lack of magnesium ions in the available crystal structures.


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Stepwise Description of the Reaction

Step 1His252 deprotonates water, which initiates a nucleophilic attack on the phosphate of the DNA in a substitution reaction which eliminates the 5' end of the DNA, with concomitant deprotonation of His134.
Step 2His134 deprotonates water, which in turn deprotonates His252 in an inferred return step.

View similar reactions (composite manual annotation)


Catalytic Residues Involved

Type Number Chain Location of Function
Tyr 76 A Side Chain
Glu 78 A Side Chain
His 134 A Side Chain
Asp 212 A Side Chain
His 252 A Side Chain

Metal Cofactors for M0041

Type Het group Number Chain
magnesium MG(not in PDB) 1 x Overview
magnesium MG(not in PDB) 2 x Overview

References

  1. S. J. Jones et al. (1996), J. Mol. Biol., 264, 1154-1163. Site-directed mutagenesis of the catalytic residues of bovine pancreatic deoxyribonuclease I.
    Medline: 9000637

Homologue information for M0041 (1dnk)

CSA Homologues

MACiE Homologues (within the PDB)

MACiE Homologues (within UniprotKB/SwissProt)



Entries with at least one Catalytic CATH code in common (different mechanisms):

MACiE Entry Enzyme Name
EC Number
PDB code CATH code Composite
Reaction Similarity
Catalytic Machinery
Similarity
M0160 exodeoxyribonuclease III
3.1.11.2
1ako 3.60.10.10
0.73330.2999Compare

Links to this entry in other databases

Link to EC-PDB-SUM Link to PDB-SUM Link to RCSB PDB Link to PDBe Link to CSA
Link to MetaCyc Link to KEGG Link to BRENDA Link to ExplorENZ
Link to EzCatDB

GOA logo
actin binding (molecular function)
endonuclease activity (molecular function)
deoxyribonuclease I activity (molecular function)
deoxyribonuclease activity (molecular function)
extracellular region (cellular component)
nucleus (cellular component)
nuclear envelope (cellular component)
DNA catabolic process (biological process)
apoptotic process (biological process)
hydrolase activity (molecular function)
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