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PDBsum entry 1c9c
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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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Free energy requirement for domain movement of an enzyme.
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Authors
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J.Ishijima,
T.Nakai,
S.Kawaguchi,
K.Hirotsu,
S.Kuramitsu.
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Ref.
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J Biol Chem, 2000,
275,
18939-18945.
[DOI no: ]
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PubMed id
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Abstract
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Domain movement is sometimes essential for substrate recognition by an enzyme.
X-ray crystallography of aminotransferase with a series of aliphatic substrates
showed that the domain movement of aspartate aminotransferase was changed
dramatically from an open to a closed form by the addition of only one CH(2) to
the side chain of the C4 substrate CH(3)(CH(2))C((alpha))H(NH(3)(+))COO(-).
These crystallographic results and reaction kinetics (Kawaguchi, S., Nobe, Y.,
Yasuoka, J., Wakamiya, T., Kusumoto, S., and Kuramitsu, S. (1997) J. Biochem.
(Tokyo) 122, 55-63; Kawaguchi, S. and Kuramitsu, S. (1998) J. Biol. Chem. 273,
18353-18364) enabled us to estimate the free energy required for the domain
movement.
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Figure 2.
Fig. 2. The mechanisms of domain movement. The  -helix 1
(Ile^17-Arg25) and the loop region (Ala^26-Ile^37) of the C3-PLP
or C4-PLP complex in the open form (these residues are colored
pink and the others gray) change to the closed form on binding
of C5-PLP or C6-PLP (colored green). Ile^17 and Ile^37 are
anchored at the active site by hydrophobic interactions with the
substrate. Leu18 is located at the N-terminal end of -helix 1
and pulls the helix into the active pocket to shield the active
site from the solvent. This tugging of residues from Ile^17 to
Ile^37 changes the enzyme from the open to the closed form.
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Figure 3.
Fig. 3. Stereoviews of AspAT bound to substrate analogs.
Only Arg292* and the substrate analogs are indicated for
clarity. a, the substrate analog is C4-PLP (the moiety of
coenzyme is labeled as PLP and that of substrate as C4). The
active-site conformation of the C4-PLP complex is almost
identical to that of substrate-free AspAT (8, 9). b, the
substrate analog is C5-PLP. Each substrate analog and the side
chain of Arg292* are superimposed onto the (F[o]  F[c]) omit
map contoured at 2.5  (a) and 3
(b) with
these atoms omitted. c, the structure of the C3-PLP complex
(magenta), C4-PLP complex (yellow), C5-PLP complex (cyan), and
C6-PLP complex (green). Note that the side chain orientation of
Arg292* changes drastically depending on substrate. These
figures were produced using the program O (23).
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2000,
275,
18939-18945)
copyright 2000.
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