 |
PDBsum entry 2dpm
|
|
|
|
|
 |
Contents |
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
* Residue conservation analysis
|
|
|
|
|
References listed in PDB file
|
|
|
Key reference
|
|
|
Title
|
|
Crystal structure of the dpnm DNA adenine methyltransferase from the dpnii restriction system of streptococcus pneumoniae bound to s-Adenosylmethionine.
|
|
|
Authors
|
|
P.H.Tran,
Z.R.Korszun,
S.Cerritelli,
S.S.Springhorn,
S.A.Lacks.
|
|
|
Ref.
|
|
Structure, 1998,
6,
1563-1575.
[DOI no: ]
|
|
|
PubMed id
|
|
|
|
|
|
Abstract
|
|
|
Background:. Methyltransferases (Mtases) catalyze the transfer of methyl groups
from S-adenosylmethionine (AdoMet) to a variety of small molecular and
macromolecular substrates. These enzymes contain a characteristic alpha/beta
structural fold. Four groups of DNA Mtases have been defined and representative
structures have been determined for three groups. DpnM is a DNA Mtase that acts
on adenine N6 in the sequence GATC; the enzyme represents group alpha DNA
Mtases, for which no structures are known. Results:. The structure of DpnM in
complex with AdoMet was determined at 1.80 A resolution. The protein comprises a
consensus Mtase fold with a helical cluster insert. DpnM binds AdoMet in a
similar manner to most other Mtases and the enzyme contains a hollow that can
accommodate DNA. The helical cluster supports a shelf within the hollow that may
recognize the target sequence. Modeling studies indicate a potential site for
binding the target adenine, everted from the DNA helix. Comparison of the DpnM
structure and sequences of group alpha DNA Mtases indicates that the group is a
genetically related family. Structural comparisons show DpnM to be most similar
to a small-molecule Mtase and then to macromolecular Mtases, although several
dehydrogenases show greater similarity than one DNA Mtase. Conclusions:. DpnM,
and by extension the DpnM family or group alpha Mtases, contains the consensus
fold and AdoMet-binding motifs found in most Mtases. Structural considerations
suggest that macromolecular Mtases evolved from small-molecule Mtases, with
different groups of DNA Mtases evolving independently. Mtases may have evolved
from dehydrogenases. Comparison of these enzymes indicates that in protein
evolution, the structural fold is most highly conserved, then function and
lastly sequence.
|
|
|
|
|
|
Figure 5.
Figure 5. The active site of DpnM showing the binding of
AdoMet and the proposed binding mode of the target adenine in
DNA. Atoms are shown in standard colors: C, black; N, blue; O,
red (except water O, white); P, purple; S, yellow. The bonds are
color coded: AdoMet, orange; adenylate residue of DNA, deep
blue; protein, green. Dashed lines indicate hydrogen bonds. For
Leu49, Phe43, Phe63 and Phe178, only mainchain atoms are shown;
for Asp194 and Trp17, only terminal parts of the sidechain are
indicated. Not all contacts are shown. (The figure was prepared
using the program MOLSCRIPT [64].)
|
|
|
|
|
|
The above figure is
reprinted
by permission from Cell Press:
Structure
(1998,
6,
1563-1575)
copyright 1998.
|
|
|
Secondary reference #1
|
|
|
Title
|
|
Crystallization of the dpnm methylase from the dpnii restriction system of streptococcus pneumoniae.
|
|
|
Authors
|
|
S.Cerritelli,
S.W.White,
S.A.Lacks.
|
|
|
Ref.
|
|
J Mol Biol, 1989,
207,
841-842.
|
|
|
PubMed id
|
|
|
|
|
|
|
|
|
Secondary reference #2
|
|
|
Title
|
|
Proteins encoded by the dpnii restriction gene cassette. Two methylases and an endonuclease.
|
|
|
Authors
|
|
A.G.De la campa,
P.Kale,
S.S.Springhorn,
S.A.Lacks.
|
|
|
Ref.
|
|
J Mol Biol, 1987,
196,
457-469.
|
|
|
PubMed id
|
|
|
|
|
|
|
|
|
Secondary reference #3
|
|
|
Title
|
|
Genetic basis of the complementary dpni and dpnii restriction systems of s. Pneumoniae: an intercellular cassette mechanism.
|
|
|
Authors
|
|
S.A.Lacks,
B.M.Mannarelli,
S.S.Springhorn,
B.Greenberg.
|
|
|
Ref.
|
|
Cell, 1986,
46,
993.
[DOI no: ]
|
|
|
PubMed id
|
|
|
|
|
|
|
|
|
Secondary reference #4
|
|
|
Title
|
|
Nucleotide sequence of the dpn ii DNA methylase gene of streptococcus pneumoniae and its relationship to the dam gene of escherichia coli.
|
|
|
Authors
|
|
B.M.Mannarelli,
T.S.Balganesh,
B.Greenberg,
S.S.Springhorn,
S.A.Lacks.
|
|
|
Ref.
|
|
Proc Natl Acad Sci U S A, 1985,
82,
4468-4472.
[DOI no: ]
|
|
|
PubMed id
|
|
|
|
|
|
|
|
|
|
|
|
|
