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PDBsum entry 1wc7
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References listed in PDB file
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Key reference
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Title
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Structure of a pseudomerohedrally twinned monoclinic crystal form of a pyridoxal phosphate-Dependent catalytic antibody.
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Author
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B.Golinelli-Pimpaneau.
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Ref.
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Acta Crystallogr D Biol Crystallogr, 2005,
61,
472-476.
[DOI no: ]
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PubMed id
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Abstract
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The purification, crystallization and structure determination at 2.3 A
resolution of the complex of the pyridoxal-5'-phosphate (PLP) dependent
catalytic antibody 15A9 with a phosphopyridoxyl-L-alanine (PPL-L-alanine)
substrate analogue are described. The crystal belongs to space group P2(1), with
two molecules in the asymmetric unit related by non-crystallographic symmetry.
The unit-cell parameters are a = 63.5, b = 81.7, c = 79.3 A and beta is
fortuitously 90 degrees . Refinement of the structure converged at unacceptably
high R factors. Although the traditional analysis of intensity distribution did
not indicate twinning, pseudomerohedral twinning was revealed by a newer test
based on local intensity differences [Padilla & Yeates (2003), Acta Cryst.
D59, 1124-1130]. When the potential twinning operator was included in SHELX, the
structure could be satisfactorily refined with a twinning fraction of 0.46,
indicating a nearly perfect hemihedrally twinned crystal. One of the active
sites is occupied by the phosphopyridoxyl-L-alanine ligand, while one iodide ion
mimics the cofactor phosphate group in the other. Four other iodide ions are
present in the structure: two are involved in specific intermolecular contacts
and two dictate the conformation of the CDRH3 loop in each molecule.
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Figure 3.
Figure 3
The iodide ions in the Fab15A9-PPL-L-Ala structure. A [sigma] [A]-weighted F[obs] -
F[calc] electron-density map omitting the iodide ions is contoured at the level of 2
[sigma] and superimposed on the active-site structures. (a) Stereoview of the
non-occupied active site of the Fab15A9-PPL-L-Ala complex. One iodide ion takes the place
of the phosphate group in one molecule of the asymmetric unit. (b) The conformation of
CDRH3 is stabilized by an iodide ion. In each molecule of the asymmetric unit, one iodide
ion makes four 3.0-3.8 Å interactions with the NH groups of His97 and His99, TrpH100e N
[epsilon] 1 and AsnH100a N [delta] 2. (c) One iodide ion interacts with the two
molecules of the asymmetric unit. At the corresponding position in the other molecule, one
iodide ion is involved in a crystallographic contact.
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The above figure is
reprinted
by permission from the IUCr:
Acta Crystallogr D Biol Crystallogr
(2005,
61,
472-476)
copyright 2005.
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Secondary reference #1
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Title
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Monoclonal antibodies against nalpha-(5'-Phosphopyridoxyl)-L-Lysine. Screening and spectrum of pyridoxal 5'-Phosphate-Dependent activities toward amino acids.
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Authors
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S.I.Gramatikova,
P.Christen.
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Ref.
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J Biol Chem, 1997,
272,
9779-9784.
[DOI no: ]
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PubMed id
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Figure 3.
Fig. 3. Acceleration of Schiff base formation by antibody
15A9. The reaction was started by the addition of 16 µM
PLP to 1^ mM N  -acetyl-L-lysine
and 2.5 µM antibody in bis-tris propane/NaCl,^ pH 7.5, at
25 °C (  ); control
reaction without antibody (  circle ).
At^ equilibrium, the difference in aldimine formed between the
control^ and the reaction in the presence of antibody apparently
corresponds^ to antibody-bound aldimine, which amounts to about
80% of the^ concentration of antibody binding sites.
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Figure 4.
Fig. 4.  ,  -Elimination
reaction of -chloroalanine
(15).
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The above figures are
reproduced from the cited reference
with permission from the ASBMB
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