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Literature summary extracted from

  • Chen, C.; Krause, K.; Pettitt, B.M.
    Advantage of being a dimer for Serratia marcescens endonuclease (2009), J. Phys. Chem. B, 113, 511-521.
    View publication on PubMedView publication on EuropePMC

Cloned(Commentary)

EC Number Cloned (Comment) Organism
3.1.30.2 molecular dynamics simulations of model-built monomer-DNA complexes and dimer-DNA complexes Serratia marcescens

KM Value [mM]

EC Number KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
3.1.30.2 additional information
-
 additional information Km is approximately related to the association constant of the enzyme and the substrate since cleavage of DNA is rate limiting Serratia marcescens

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
3.1.30.2 Mg2+
-
 Serratia marcescens

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
3.1.30.2 DNA + H2O Serratia marcescens protein and DNA are held together by a mix of salt-bridges, water-mediated and direct hydrogen bond interactions between the protein and DNA backbone, almost no DNA bases are directly involved in the contacts ?
-
 ?

Organism

EC Number Organism UniProt Comment Textmining
3.1.30.2 Serratia marcescens P13717
-
-

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
3.1.30.2 DNA + H2O protein and DNA are held together by a mix of salt-bridges, water-mediated and direct hydrogen bond interactions between the protein and DNA backbone, almost no DNA bases are directly involved in the contacts Serratia marcescens ?
-
 ?

Subunits

EC Number Subunits Comment Organism
3.1.30.2 homodimer each monomer consists of 245 amino acids, they function independently of each other, monomer and dimer can function with same specific activity. Dimer form has an electrostatic advantage over the monomer to associate with DNA, inner-sphere binding in the monomer, outer-sphere in the dimer, interface of the protein and DNA is full of charged side chains, such as Arg57, Arg87, Arg125, Arg196, and Mg2+. Interfacial region is highly hydrated with an average of 27 hydration sites in the monomer (water acts more to screen the electrostatic region between the monomer and DNA) and 31 sites in the dimer (water acts more as a glue to provide structural adaptability with the protein and DNA). Dynamics of H-bonds of water in this active centre only little difference is found (water in the working region in the dimer complex has larger fluctuations than in monomer). Dimerization leads to different contacts between DNA and protein residues, especially to Mg2+ Serratia marcescens

Synonyms

EC Number Synonyms Comment Organism
3.1.30.2 Serratia marcescens endonuclease SMnase Serratia marcescens