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Literature summary for 3.1.30.2 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
Search for more literature for 3.1.30.2

Cloned(Commentary)

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

KM Value [mM]

KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
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

Metals/Ions Comment Organism Structure
Mg2+
-
 Serratia marcescens

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
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

Organism UniProt Comment Textmining
Serratia marcescens P13717
-
-

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
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

Subunits Comment Organism
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

Synonyms Comment Organism
Serratia marcescens endonuclease SMnase Serratia marcescens