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PDBsum entry 1n2m
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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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Pyruvoyl-Dependent arginine decarboxylase from methanococcus jannaschii: crystal structures of the self-Cleaved and s53a proenzyme forms.
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Authors
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W.D.Tolbert,
D.E.Graham,
R.H.White,
S.E.Ealick.
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Ref.
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Structure, 2003,
11,
285-294.
[DOI no: ]
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PubMed id
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Abstract
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The three-dimensional structure of pyruvoyl-dependent arginine decarboxylase
from Methanococcus jannaschii was determined at 1.4 A resolution. The pyruvoyl
group of arginine decarboxylase is generated by an autocatalytic internal
serinolysis reaction at Ser53 in the proenzyme resulting in two polypeptide
chains. The structure of the nonprocessing S53A mutant was also determined. The
active site of the processed enzyme unexpectedly contained the reaction product
agmatine. The crystal structure confirms that arginine decarboxylase is a
homotrimer. The protomer fold is a four-layer alphabetabetaalpha sandwich with
topology similar to pyruvoyl-dependent histidine decarboxylase. Highly conserved
residues Asn47, Ser52, Ser53, Ile54, and Glu109 are proposed to play roles in
the self-processing reaction. Agmatine binding residues include the C terminus
of the beta chain (Ser52) from one protomer and the Asp35 side chain and the
Gly44 and Val46 carbonyl oxygen atoms from an adjacent protomer. Glu109 is
proposed to play a catalytic role in the decarboxylation reaction.
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Figure 3.
Figure 3. Stereo View of the Active Site of PvlArgDCThe
product agamatine and key residues are shown as ball-and-stick
models. Electron density is shown for the agmatine molecule and
the pyruvoyl group. Key hydrogen bonds between agmatine and the
protein are shown as dashed lines and the donor-acceptor
distances are labeled. The figure was generated with BOBSCRIPT
[44 and 45] and Raster3D [46].
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The above figure is
reprinted
by permission from Cell Press:
Structure
(2003,
11,
285-294)
copyright 2003.
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Secondary reference #1
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Title
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Methanococcus jannaschii uses a pyruvoyl-Dependent arginine decarboxylase in polyamine biosynthesis.
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Authors
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D.E.Graham,
H.Xu,
R.H.White.
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Ref.
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J Biol Chem, 2002,
277,
23500-23507.
[DOI no: ]
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PubMed id
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Figure 1.
Fig. 1. Condensation of ONBH with the pyruvoyl group in
the  -subunit of
M. jannaschii PvlArgDC produces an oxime derivative. Cleavage by
cyanogen bromide and opening of the homoserine lactone ring
results in a small polypeptide that was detected by LC-ESI-MS
(MH+ = 453 m/z).
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Figure 3.
Fig. 3. Initial rates of ArgDC activity at varying
concentrations of L-arginine. Activity profiles of PvlArgDC were
measured at 83 °C (  circle )
and at 70 °C (  ).
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The above figures are
reproduced from the cited reference
with permission from the ASBMB
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