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211 a.a.
205 a.a.
_ZN
Key reference
DOI no: 10.1006/jmbi.1998.2025 J Mol Biol 282:1033-1041 (1998) PubMed id: 9753552
A comparison of the crystallographic structures of two catalytic antibodies with esterase activity. J.L.Buchbinder, R.C.Stephenson, T.S.Scanlan, R.J.Fletterick. ABSTRACT
The crystallographic structure of the Fab fragment of the catalytic antibody, 29G11, complexed with an (S)-norleucine phenyl phosphonate transition state analog was determined at 2.2 A resolution. The antibody catalyzes the hydrolysis of norleucine phenyl ester with (S)-enantioselectivity. The shape and charge complementarity of the binding pocket for the hapten account for the preferential binding of the (S)-enantiomer of the substrate. The structure is compared to that of the more catalytically efficient antibody, 17E8, induced by the same hapten transition state analog. 29G11 has different residues from 17E8 at eight positions in the heavy chain, including four substitutions in the hapten-binding pocket: A33V, S95G, S99R and Y100AN, and four substitutions at positions remote from the catalytic site, I28T, R40K, V65G and F91L. The two antibodies show large differences in the orientations of their variable and constant domains, reflected by a 32 degrees difference in their elbow angles. The VL and VH domains in the two antibodies differ by a rotation of 8.8 degrees. The hapten binds in similar orientations and locations in 29G11 and 17E8, which appear to have catalytic groups in common, though the changes in the association of the variable domains affect the precise positioning of residues in the hapten-binding pocket.
Selected figure(s)
Figure 2.
Figure 2. Stereo view of the 2Fo - Fc electron density map contoured at 1.0 s shows the region in the vicinity of the hapten at the catalytic site of 29G11. The hapten is colored yellow. This Figure was prepared with the program O (Jones et al., 1991).Figure 4.
Figure 4. View of hapten-binding site. Residues within 4.2 Å of the hapten are shown. Arg L96 forms hydrogen bonds with the amide carbonyl oxygen atom, the pro-R phosphonate oxygen atom, and the bridging phosphonate oxygen atom of the hapten. Charged hydrogen bonds are formed between the NH3 group of Lys H93 and the pro-S phosphonate oxygen atom of the hapten. The norleucine side-chain of the hapten is sur- rounded by the hydrophobic residues: Tyr L36, Leu L46, Leu L89 and Tyr L91. Recognition of the phenyl ring of the hapten is mediated by the aromatic residues Phe L98, Tyr L36, Trp H47 and Trp H103.The above figures are reprinted by permission from Elsevier: J Mol Biol (1998, 282, 1033-1041) copyright 1998. Figures were selected by the author.
Literature references that cite this PDB file's key reference
PubMed id Reference
18326040 K.Tsumoto, A.Yokota, Y.Tanaka, M.Ui, T.Tsumuraya, I.Fujii, I.Kumagai, Y.Nagumo, H.Oguri, M.Inoue, and M.Hirama (2008).
Critical contribution of aromatic rings to specific recognition of polyether rings. The case of ciguatoxin CTX3C-ABC and its specific antibody 1C49.J Biol Chem, 283, 12259-12266.
PDB code: 2e27
12824485 G.J.Kroon, H.Mo, M.A.Martinez-Yamout, H.J.Dyson, and P.E.Wright (2003).
Changes in structure and dynamics of the Fv fragment of a catalytic antibody upon binding of inhibitor.Protein Sci, 12, 1386-1394.
11913392 D.J.Tantillo, and K.N.Houk (2002).
Transition state docking: a probe for noncovalent catalysis in biological systems. Application to antibody-catalyzed ester hydrolysis.J Comput Chem, 23, 84-95.
11468416 T.A.Muranova, S.N.Ruzheinikov, S.E.Sedelnikova, A.Moir, L.J.Partridge, H.Kakinuma, N.Takahashi, K.Shimazaki, J.Sun, Y.Nishi, and D.W.Rice (2001).
The preparation and crystallization of Fab fragments of a family of mouse esterolytic catalytic antibodies and their complexes with a transition-state analogue.Acta Crystallogr D Biol Crystallogr, 57, 1192-1195. The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.
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