1H8S

Three-dimensional structure of anti-ampicillin single chain Fv fragment complexed with the hapten.

Summary for 1H8S

• Entry DOI: 10.2210/pdb1h8s/pdb
• Related: 1H8N 1H8O
• Descriptor: MUTANT AL2 6E7P9G, (2S,5R,6R)-6-{[(2R)-2-AMINO-2-PHENYLETHANOYL]AMINO}-3,3-DIMETHYL-7-OXO-4-THIA-1-AZABICYCLO[3.2.0]HEPTANE-2-CARBOXYLIC ACID, SULFATE ION, ... (4 entities in total)
• Functional Keywords: anti-ampicillin antibodies
• Biological source: MUS MUSCULUS
• Total number of polymer chains: 2
• Total formula weight: 54555.00

Authors

Burmester, J.,Spinelli, S.,Pugliese, L.,Krebber, A.,Honegger, A.,Jung, S.,Schimmele, B.,Cambillau, C.,Pluckthun, A. (deposition date: 2001-02-15, release date: 2001-08-02, Last modification date: 2024-11-20)

Primary citation

Burmester, J.,Spinelli, S.,Pugliese, L.,Krebber, A.,Honegger, A.,Jung, S.,Schimmele, B.,Cambillau, C.,Pluckthun, A.
Selection, Characterization and X-Ray Structure of Anti-Ampicillin Single-Chain Fv Fragments from Phage-Displayed Murine Antibody Libraries
J.Mol.Biol., 309:671-, 2001

PubMed Abstract: Single-chain Fv (scFv) antibody libraries were constructed from mice immunized with an ampicillin-bovine serum albumin conjugate. Several antibodies with specificity for intact ampicillin were selected by phage display and characterized. The antibody scFv fragment aL2 binds to intact ampicillin and shows no detectable cross-reactivity with hydrolyzed ampicillin. We determined the X-ray structures of two crystal forms of w.t. aL2, which differ mainly in the side-chain conformation of Trp H109 (according to a new consensus nomenclature Kabat residue number H95) in the extremely short (three residues) CDR H3 and the presence or absence of a well-resolved molecule of 2-methyl-pentane-2,4-diol in the bottom of the binding pocket. Attempts to co-crystallize aL2 with its antigen or to diffuse ampicillin into the wild-type aL2 crystals were unsuccessful, since crystal contacts obstruct the binding pocket. However, a mutant with two point mutations near the N terminus (Gln H6 replaced by Glu and Ala H10 (Kabat H9) replaced by Gly) crystallized in a form compatible with antigen-binding. Although the mutations affect the conformation of framework I, the conformations of the binding pocket of the uncomplexed wild-type aL2 and of the mutant complex were almost identical. The structure explains the specificity of the antibody for intact ampicillin and the degree of cross-reactivity of aL2 with a wide variety of ampicillin analogs. This antibody system will be very useful as a diagnostic reagent for antibiotics use and abuse, as a model for the effect of expression of antibiotic binding molecules in Escherichia coli, and for directed evolution towards high antibiotic resistance.

PubMed: 11397088
DOI: 10.1006/JMBI.2001.4663

Experimental method

X-RAY DIFFRACTION (2.4 Å)