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PDBsum entry 1mrf
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Immunoglobulin
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PDB id
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1mrf
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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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Preparation, Characterization and crystallization of an antibody FAB fragment that recognizes RNA. Crystal structures of native FAB and three FAB-Mononucleotide complexes.
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Authors
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P.R.Pokkuluri,
F.Bouthillier,
Y.Li,
A.Kuderova,
J.Lee,
M.Cygler.
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Ref.
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J Mol Biol, 1994,
243,
283-297.
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PubMed id
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Abstract
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Fab fragments from Jel 103, an antibody which specifically binds to
single-stranded poly(rl), were prepared by papain digestion, separated into
eight isoforms and characterized by mass spectrometry. One of the purified
isoforms yielded crystals suitable for structural studies by X-ray diffraction
and its crystal structure was determined to 2.4 A resolution. Soaking the
crystals in solutions containing either of the mononucleotides
inosine-5'-diphosphate, guanosine-5'-diphosphate or
deoxyinosine-5'-monophosphate resulted in binding of the nucleotide in a single
binding site. However, adenosine-5'-diphosphate does not bind to this antibody.
The recognition of the base is achieved through hydrogen bonds to the C6
carbonyl oxygen and the imino NH group of the purine in a pattern similar to
that of the base-base interactions in a double-stranded nucleic acid. Additional
binding energy is provided by stacking of the base and the Tyr32L side-chain and
by interaction of the alpha-phosphate with the antibody in an anionic binding
site. Most of the side-chains interacting with the nucleotide come from the
light chain. Surprisingly, this antibody shares the VL sequence with another
nucleic acid-binding antibody, BV04-1. The latter binds to a single stranded DNA
with a high preference for thymine bases. The structures of the unliganded and
complexed Jel 103 Fab are compared to those of BV-04-1 Fab and while they show
similarity in recognition of the base of the immunodominant nucleotide, their 5'
phosphates occupy different positions, suggesting different orientation of the
nucleic acid bound to these two antibodies. Differences in the conformations of
the L1 loops between the two Fabs have been noted.
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