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PDBsum entry 1smn
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* Residue conservation analysis
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Enzyme class:
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E.C.3.1.30.2
- Serratia marcescens nuclease.
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Reaction:
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Endonucleolytic cleavage to 5'-phosphomononucleotide and 5'-phosphooligonucleotide end-products.
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DOI no:
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Protein Sci
5:24-33
(1996)
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PubMed id:
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Identification of the Serratia endonuclease dimer: structural basis and implications for catalysis.
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M.D.Miller,
K.L.Krause.
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ABSTRACT
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The Serratia endonuclease is an extracellularly secreted enzyme capable of
cleaving both single- and double-stranded forms of DNA and RNA. It is the first
member of a large class of related and usually dimeric endonucleases for which a
structure is known. Using X-ray crystallography, the structure of monomer of
this enzyme was reported by us previously (Miller MD et al., 1994, Nature Struct
Biol 1:461-468). We now confirm the dimeric nature of this enzyme through
light-scattering experiments and identify the physiologic dimer interface
through crystal packing analysis. This dimerization occurs through an isologous
twofold interaction localized to the carboxy-terminal subdomain of the enzyme.
The dimer is a prolate ellipsoid with dimensions 30 A x 35 A x 90 A. The dimer
interface is flat and contains four salt links, several hydrogen bonds, and
nonpolar interactions. Buried water is prominent in this interface and it
includes an unusual "cubic" water cluster. The position of the two active sites
in the dimer suggests that they can act independently in their cleavage of DNA,
but have a geometrical advantage in attacking substrate relative to the monomer.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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S.H.Chan,
L.Opitz,
L.Higgins,
D.O'loane,
and
S.Y.Xu
(2010).
Cofactor requirement of HpyAV restriction endonuclease.
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PLoS One,
5,
e9071.
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B.Loll,
M.Gebhardt,
E.Wahle,
and
A.Meinhart
(2009).
Crystal structure of the EndoG/EndoGI complex: mechanism of EndoG inhibition.
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Nucleic Acids Res,
37,
7312-7320.
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PDB code:
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C.Temme,
R.Weissbach,
H.Lilie,
C.Wilson,
A.Meinhart,
S.Meyer,
R.Golbik,
A.Schierhorn,
and
E.Wahle
(2009).
The Drosophila melanogaster Gene cg4930 Encodes a High Affinity Inhibitor for Endonuclease G.
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J Biol Chem,
284,
8337-8348.
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C.Chen,
B.W.Beck,
K.Krause,
T.E.Weksberg,
and
B.M.Pettitt
(2007).
Effects of dimerization of Serratia marcescens endonuclease on water dynamics.
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Biopolymers,
85,
241-252.
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C.Chen,
B.W.Beck,
K.Krause,
and
B.M.Pettitt
(2006).
Solvent participation in Serratia marcescens endonuclease complexes.
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Proteins,
62,
982-995.
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F.Rodier,
R.P.Bahadur,
P.Chakrabarti,
and
J.Janin
(2005).
Hydration of protein-protein interfaces.
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Proteins,
60,
36-45.
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E.S.Rangarajan,
and
V.Shankar
(2001).
Sugar non-specific endonucleases.
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FEMS Microbiol Rev,
25,
583-613.
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M.Drouin,
P.Lucas,
C.Otis,
C.Lemieux,
and
M.Turmel
(2000).
Biochemical characterization of I-CmoeI reveals that this H-N-H homing endonuclease shares functional similarities with H-N-H colicins.
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Nucleic Acids Res,
28,
4566-4572.
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J.W.Pflugrath
(1999).
The finer things in X-ray diffraction data collection.
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Acta Crystallogr D Biol Crystallogr,
55,
1718-1725.
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M.J.Benedik,
and
U.Strych
(1998).
Serratia marcescens and its extracellular nuclease.
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FEMS Microbiol Lett,
165,
1.
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J.Antosiewicz,
M.D.Miller,
K.L.Krause,
and
J.A.McCammon
(1997).
Simulation of electrostatic and hydrodynamic properties of Serratia endonuclease.
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Biopolymers,
41,
443-450.
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P.Friedhoff,
B.Kolmes,
O.Gimadutdinow,
W.Wende,
K.L.Krause,
and
A.Pingoud
(1996).
Analysis of the mechanism of the Serratia nuclease using site-directed mutagenesis.
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Nucleic Acids Res,
24,
2632-2639.
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P.Friedhoff,
G.Meiss,
B.Kolmes,
U.Pieper,
O.Gimadutdinow,
C.Urbanke,
and
A.Pingoud
(1996).
Kinetic analysis of the cleavage of natural and synthetic substrates by the Serratia nuclease.
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Eur J Biochem,
241,
572-580.
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Y.Suh,
S.Jin,
T.K.Ball,
and
M.J.Benedik
(1996).
Two-step secretion of the Serratia marcescens extracellular nuclease.
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J Bacteriol,
178,
3771-3778.
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
code is
shown on the right.
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Links
