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Overview for MACiE Entry M0042

Version history

General Information

EC Number: 3.1.30.2 (A member of the Hydrolases, Acting on ester bonds, Endoribonucleases that are active with either ribo- or deoxyribonucleic acids and produce 5'-phosphomonoesters)

Enzyme Name: nuclease

Biological Species: Serratia marcescens (Bacteria)

Catalytic Chain UniprotKB Accession Codes:

Representative PDB Code: 1ql0 - SM ENDONUCLEASE FROM SERATIA MARCENSCENS AT ATOMICRESOLUTION (Resolution = 1.1 Å).

Catalytic CATH Codes:

"Other" 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

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Stepwise Description of the Reaction

Step 1His89 deprotonates water, which initiates a nucleophilic attack on the phosphate of the DNA, forming a pentavalent intermediate in an addition reaction.
Step 2The pentavalent intermediate collapses, eliminating the 3'-hydroxyl of the DNA, which deprotonates water, which in turn deprotonates His89.

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Catalytic Residues Involved

Type Number Chain Location of Function
Arg 57 A Side Chain
His 89 A Side Chain
Asn 119 A Side Chain
Glu 127 A Side Chain

Metal Cofactors for M0042

Type Het group Number Chain
magnesium MG 300 A Overview

References

  1. S. V. Shlyapnikov et al. (2000), Acta Cryst., D56, 567-572. Atomic structure of the Serratia marcescens endonuclease at 1.1 A resolution and the enzyme reaction mechanism.
    Medline: 10771425
  2. M. D. Miller et al. (1999), J. Mol. Biol., 288, 975-987. The active site of Serratia endonuclease contains a conserved magnesium-water cluster.
    Medline: 10329193

Homologue information for M0042 (1ql0)

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
Link to EzCatDB

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nucleic acid binding (molecular function)
nuclease activity (molecular function)
endonuclease activity (molecular function)
extracellular region (cellular component)
hydrolase activity (molecular function)
metal ion binding (molecular function)
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