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Catalytic Site Atlas

CSA LITERATURE entry for 1smn

E.C. nameSerratia marcescens nuclease
SpeciesSerratia marcescens (Bacteria)
E.C. Number (IntEnz)
CSA Homologues of 1smn1g8t,1qae,1ql0,1zm8,2o3b,3ism,
CSA Entries With UniProtID P13717
CSA Entries With EC Number
PDBe Entry 1smn
PDBSum Entry 1smn
MACiE Entry M0042

Literature Report

Introduction Serratia endonuclease is of particular interest because of its broad specificity, high activity and chemical stability. In addition antiviral and antitumor properties have been attributed to this enzyme.
It acts without any apparent base preference and cleaves both single- and double - stranded DNA and RNA. Functionally, the enzyme is similar to DNase I as they are both magnesium-dependent endonucleases that catalyse the cleavage of 3'O-P bond. Although functional similarities exist, Serratia nuclease structure contrasts sharply with the protein fold observed in DNase I.
Magnesium is important for activity, absence of magnesium significantly reduces the activity of the nuclease. The nuclease DNA-binding site is located between two main amino and carboxy-terminal structural domains of the protein, the DNA binding cleft is flanked by two rows of positively charged amino acids that could interact with about one full turn of DNA B-form. This cleft contains among other cationic amino acids, the invariant catalytic residues of ARG 87 and ARG 131, and also contains HIS 89 and GLU 127.
HIS 89 and GLU 127 have emerged as strong candidates for direct participation in the chemistry of the nuclease reaction.
Mechansim HIS 89 and GLU 127 are both potential participants in the nucleasereaction. It has been postulated that HIS 89 serves as a general acid and GLU 127 serves as either a nucleophile or a general base. Phosphodiesters are hydrolysed via nucleophilic attack by a water molecule forming a penta-coordinated trigonal bipyramid intermediate.

Catalytic Sites for 1smn

Annotated By Reference To The Literature - Site 1 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription

Annotated By Reference To The Literature - Site 2 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription

Literature References

Shlyapnikov SV
Atomic structure of the Serratia marcescens endonuclease at 1.1 A resolution and the enzyme reaction mechanism.
Acta Crystallogr D Biol Crystallogr 2000 56 567-572
PubMed: 10771425
Miller MD.
2.1 A structure of Serratia endonuclease suggests a mechanism for binding to double-stranded DNA
Nat Struct Biol 1994 1 461-468
PubMed: 7664065
Lunin VY.
Three-dimensional structure of Serratia marcescens nuclease at 1.7 A resolution and mechanism of its action
FEBS Lett 1997 412 217-222
PubMed: 9257723