Summary for 2JEL
| Entry DOI | 10.2210/pdb2jel/pdb |
| Descriptor | JEL42 FAB FRAGMENT, HISTIDINE-CONTAINING PROTEIN, SULFATE ION, ... (5 entities in total) |
| Functional Keywords | antibody-protein complex, histidine-containing protein, molecular recognition, complex (antibody-antigen), complex (antibody-antigen) complex, complex (antibody/antigen) |
| Biological source | Mus musculus (house mouse) More |
| Cellular location | Cytoplasm: P0AA04 |
| Total number of polymer chains | 3 |
| Total formula weight | 56275.98 |
| Authors | Prasad, L.,Waygood, E.B.,Lee, J.S.,Delbaere, L.T.J. (deposition date: 1998-02-24, release date: 1998-05-27, Last modification date: 2024-04-03) |
| Primary citation | Prasad, L.,Waygood, E.B.,Lee, J.S.,Delbaere, L.T.J. The 2.5 A resolution structure of the jel42 Fab fragment/HPr complex J.Mol.Biol., 280:829-845, 1998 Cited by PubMed Abstract: The tertiary structure of Jel42 Fab fragment complexed with HPr, a phosphocarrier protein of the phosphoenolpyruvate:sugar phosphotransferase system of Escherichia coli, has been determined at 2.5 A resolution. X-ray diffraction from a larger crystal provided 22,067 unique reflections as compared to 14,763 unique reflections (2.8 A resolution), which were obtained previously from a smaller crystal. The higher resolution allowed for more precise location of amino acid side-chains and for the location of well-ordered water molecules. Five more residues in the Fab fragment are found to be involved in binding HPr and two additional residues are identified as part of the epitope, bringing the totals to 24 and 16, respectively. At least nine water molecules are found at the interface between the two proteins, and these mediate hydrogen bonding interactions between the Fab fragment and HPr. Three additional hydrogen bonds have been identified (bringing the total to ten) and one salt-bridge occurs between LysL50 of the L2 complementarity-determining region (CDR) and GluP66 of HPr. This salt-bridge is the only interaction between HPr and CDRL2; thus all six CDRs are involved in binding. Inspection and empirical energy minimization of mutant HPrs in the complex indicate that, in some cases in the binding interaction, water molecules may compensate for residue alterations. Binding to the mutant SerP64Tyr HPr may require a movement of the HPr main chain. The active centre region of HPr, which is not involved in binding the antibody, and which was not resolved in the 2.8 A resolution structure of the complex, was determined. This active centre determined at pH 5.8, which is completely free of intermolecular contacts due to crystal packing, shows a potential hydrogen bond between the AsnP12 OD1 atom and the HisP15 NE2 atom, and no involvement of the C terminus with HisP15. The HisP15 ND1 atom is the site of phosphorylation in HPr. Although a specific amino acid at residue 12 is not conserved in HPr molecules from all species, a hydrogen bond between the side-chains of residue 12 and HisP15 may be a conserved feature of the active centres. PubMed: 9671553DOI: 10.1006/jmbi.1998.1888 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.5 Å) |
Structure validation
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