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PDBsum entry 1xgn
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Aminopeptidase
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PDB id
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1xgn
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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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Crystal structure of methionine aminopeptidase from hyperthermophile, Pyrococcus furiosus.
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Authors
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T.H.Tahirov,
H.Oki,
T.Tsukihara,
K.Ogasahara,
K.Yutani,
K.Ogata,
Y.Izu,
S.Tsunasawa,
I.Kato.
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Ref.
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J Mol Biol, 1998,
284,
101-124.
[DOI no: ]
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PubMed id
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Note In the PDB file this reference is
annotated as "TO BE PUBLISHED".
The citation details given above were identified by an automated
search of PubMed on title and author
names, giving a
perfect match.
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Abstract
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The structure of methionine aminopeptidase from hyperthermophile Pyrococcus
furiosus (PfMAP) with an optimal growth temperature of 100 degreesC was
determined by the multiple isomorphous replacement method and refined in three
different crystal forms, one monoclinic and two hexagonal, at resolutions of
2.8, 2.9, and 3.5 A. The resolution of the monoclinic crystal form was extended
to 1.75 A by water-mediated transformation to a low-humidity form, and the
obtained diffraction data used for high-resolution structure refinement. This is
the first description of a eukaryotic type methionine aminopeptidase structure.
The PfMAP molecule is composed of two domains, a catalytic domain and an
insertion domain, connected via two antiparallel beta-strands. The catalytic
domain, which possesses an internal 2-fold symmetry and contains two cobalt ions
in the active site, resembles the structure of a prokaryotic type MAP from
Escherichia coli (EcMAP), while the structure of the insertion domain containing
three helices has a novel fold and accounts for a major difference between the
eukaryotic and prokaryotic types of methionine aminopeptidase. Analysis of the
PfMAP structure in comparison with EcMAP and other mesophile proteins reveals
several factors which may contribute to the hyperthermostability of PfMAP: (1) a
significantly high number of hydrogen bonds and ion-pairs between side-chains of
oppositely charged residues involved in the stabilization of helices; (2) an
increased number of hydrogen bonds between the positively charged side-chain and
neutral oxygen; (3) a larger number of buried water molecules involved in
crosslinking the backbone atoms of sequentially separate segments; (4)
stabilization of two antiparallel beta-strands connecting the two domains of the
molecule by proline residues; (5) shortening of N and C-terminal tails and
stabilization of the loop c3E by deletion of three residues.
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Figure 2.
Figure 2. The arrangement of proline residues Pro201,
Pro202, and Pro266 in strands c2 and c3. Hydrogen bonds are
shown by broken lines.
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Figure 6.
Figure 6. Ion-pairs (a) in PfMAP, molecule lhf-A1, and (b)
EcMAP. The a-carbon traces are shown by thin continuous lines,
and the side-chains of charged residues forming the ion-pairs
are shown by continuous bold lines. The interactions between the
oppositely charged atoms with distance cutoff of 4 Å
(broken lines).
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(1998,
284,
101-124)
copyright 1998.
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Secondary reference #1
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Title
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Crystallization and preliminary X-Ray analysis of methionine aminopeptidase from the hyperthermophilic bacterium pyrococcus furiosus.
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Authors
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T.H.Tahirov,
H.Oki,
T.Tsukihara,
K.Ogasahara,
Y.Izu,
S.Tsunasawa,
I.Kato,
K.Yutani.
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Ref.
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Acta Crystallogr D Biol Crystallogr, 1997,
53,
798-801.
[DOI no: ]
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PubMed id
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Figure 1.
Fig. 1. Photomicrographs for crystalline MAP-Pfu for (a) form A, (b)
form B and (c) form C or D.
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The above figure is
reproduced from the cited reference
with permission from the IUCr
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