spacer

Overview for MACiE Entry M0165

Version history

General Information

EC Number: 3.1.31.1 (A member of the Hydrolases, Acting on ester bonds, Endoribonucleases that are active with either ribo- or deoxyribonucleic acids and produce 3'-phosphomonoesters)

Enzyme Name: micrococcal nuclease

Biological Species: Staphylococcus aureus (Bacteria)

Catalytic Chain UniprotKB Accession Codes:

Representative PDB Code: 2sns - STAPHYLOCOCCAL NUCLEASE. PROPOSED MECHANISM OF ACTION BASEDON STRUCTURE OF ENZYME-THYMIDINE 3(PRIME),5(PRIME)-BIPHOSPHATE-CALCIUM ION COMPLEX AT 1.5-ANGSTROMS RESOLUTION (Resolution = 1.50 Å).

Catalytic CATH Codes:

  • 2.40.50.90 - OB fold (Dihydrolipoamide Acetyltransferase, E2P)

Display structure information

Overall Reaction:

Image of DNA

Image of water

right arrow

Image of DNA 3-phosphate

Image of DNA 5-hydroxyl

DNA
C00039
CHEBI:4705
water
C00001
CHEBI:15377
DNA 3-phosphate
X00064
DNA 5-hydroxyl
X00065

Overall Comment: This enzyme acts in both DNA and RNA.


View similar reactions


Stepwise Description of the Reaction

Step 1Glu43 deprotonates the calcium activated water molecule, which then attacks the DNA phosphate bond in a nucleophilic substitution. The 3' DNA hydroxyl protonates from Arg87.
Step 2Arg87 deprotonates water in an inferred step.

View similar reactions (composite manual annotation)


Catalytic Residues Involved

Type Number Chain Location of Function
Arg 35 A Side Chain
Glu 43 A Side Chain
Arg 87 A Side Chain

Metal Cofactors for M0165

Type Het group Number Chain
calcium CA 1 x Overview

References

  1. F. A. Cotton et al. (1979), Proc. Natl Acad. Sci. USA, 76, 2551-2555. Staphylococcal nuclease: proposed mechanism of action based on structure of enzyme-thymidine 3',5'-bisphosphate-calcium ion complex at 1.5-A resolution.
    Medline: 288045
  2. E. H. Serpersu et al. (1987), Biochemistry, 26, 1289-1300. Kinetic and magnetic resonance studies of active-site mutants of staphylococcal nuclease: factors contributing to catalysis.
    Medline: 3567171
  3. D. J. Weber et al. (1992), Proteins, 13, 275-287. NMR docking of a substrate into the X-ray structure of staphylococcal nuclease.
    Medline: 1518799

Homologue information for M0165 (2sns)

CSA Homologues

MACiE Homologues (within the PDB)

MACiE Homologues (within UniprotKB/SwissProt)


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

GOA logo
nucleic acid binding (molecular function)
nuclease activity (molecular function)
endonuclease activity (molecular function)
extracellular region (cellular component)
membrane (cellular component)
hydrolase activity (molecular function)
hydrolase activity, acting on ester bonds (molecular function)
metal ion binding (molecular function)
spacer
spacer