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PDBsum entry 1obj
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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Characterization of a novel ser-Cisser-Lys catalytic triad in comparison with the classical ser-His-Asp triad.
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Authors
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S.Shin,
Y.S.Yun,
H.M.Koo,
Y.S.Kim,
K.Y.Choi,
B.H.Oh.
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Ref.
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J Biol Chem, 2003,
278,
24937-24943.
[DOI no: ]
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PubMed id
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Abstract
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Amidase signature family enzymes, which are widespread in nature, contain a
newly identified Ser-cisSer-Lys catalytic triad in which the peptide bond
between Ser131 and the preceding residue Gly130 is in a cis configuration. In
order to characterize the property of the novel triad, we have determined the
structures of five mutant malonamidase E2 enzymes that contain a Cys-cisSer-Lys,
Ser-cisAla-Lys, or Ser-cisSer-Ala triad or a substitution of Gly130 with
alanine. Cysteine cannot replace the role of Ser155 due to a hyper-reactivity of
the residue, which results in the modification of the cysteine to cysteinyl
sulfinic acid, most likely inside the expression host cells. The lysine residue
plays a structural as well as a catalytic role, since the substitution of the
residue with alanine disrupts the active site structure completely. The two
observations are in sharp contrast with the consequences of the corresponding
substitutions in the classical Ser-His-Asp triad. Structural data on the mutant
containing the Ser-cisAla-Lys triad convincingly suggest that Ser131 plays an
analogous catalytic role as the histidine of the Ser-His-Asp triad. The unusual
cis configuration of Ser131 appears essential for the precise contacts of this
residue with the other triad residues, as indicated by the near invariance of
the preceding glycine residue (Gly130), structural data on the G130A mutant, and
by a modeling experiment. The data provide a deep understanding of the role of
each residue of the new triad at the atomic level and demonstrate that the new
triad is a catalytic device distinctively different from the classical triad or
its variants.
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Figure 5.
FIG. 5. G130A mutation fails to maintain a structured loop.
A stereo view of the 2F[o]-F[c] map (2.2 Å, 1  ) of the
G130A mutant is shown for the active site. Although Ala^130 was
included in the final refinement and map calculation, electron
density for this residue is only partly visible.
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Figure 6.
FIG. 6. K62A mutation disrupts the active site. a,
2F[o]-F[c] electron density map for the active site of the K62A
mutant. The map was calculated to 2.0 Å and contoured at
1.5 . Two tightly bound
water molecules, Wat942 and Wat941, indicated as Wat1 and Wat2,
are absent in the wild-type MAE2 structure. The hydrogen bonds
present only in the mutant structure are shown in dotted lines.
b, superposition of the active sites. The catalytic components
of the wild-type (in coral) and K62A mutant (in blue) enzymes
are superimposed. The circles indicate the positions of the
Ser155 in the two structures. Unlike the oxyanion
hole-containing segment, the cisSer131-containing loop undergoes
a minor conformational change. Figs. 1, 2, 3, 4, 5, 6 were
prepared using the program BobScript and rendered using Raster3D.
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2003,
278,
24937-24943)
copyright 2003.
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