Redesign of LAOBP to bind novel l-amino acid ligands.
Abstract
Computational protein design is still a challenge for advancing structure-function relationships. While recent advances in this field are promising, more information for genuine predictions is needed. Here, we discuss different approaches applied to install novel glutamine (Gln) binding into the Lysine/Arginine/Ornithine binding protein (LAOBP) from Salmonella typhimurium. We studied the ligand binding behavior of two mutants: a binding pocket grafting design based on a structural superposition of LAOBP to the Gln binding protein QBP from Escherichia coli and a design based on statistical coupled positions. The latter showed the ability to bind Gln even though the protein was not very stable. Comparison of both approaches highlighted a nonconservative shared point mutation between LAOBP_graft and LAOBP_sca. This context dependent L117K mutation in LAOBP turned out to be sufficient for introducing Gln binding, as confirmed by different experimental techniques. Moreover, the crystal structure of LAOBP_L117K in complex with its ligand is reported.
Submission Details
ID: TZNnHzq24
Submitter: Jesus Banda-Vazquez
Submission Date: May 5, 2020, 10:44 a.m.
Version: 1
Publication Details
Banda-Vázquez J;Shanmugaratnam S;Rodríguez-Sotres R;Torres-Larios A;Höcker B;Sosa-Peinado A,Protein Sci (2018) Redesign of LAOBP to bind novel l-amino acid ligands. PMID:29524280Additional Information
Study Summary
| Number of data points | 72 |
| Proteins | Lysine/arginine/ornithine-binding periplasmic protein |
| Unique complexes | 9 |
| Assays/Quantities/Protocols | Experimental Assay: Kd ; Experimental Assay: dH ; Experimental Assay: -TdS ; Experimental Assay: dG ; Derived Quantity: SD of dG ; Derived Quantity: SD of -TdS ; Derived Quantity: SD of dH ; Derived Quantity: SD of Kd |
| Libraries | Dissociation Constants and Thermodynamic Values for Selected Ligands |
Structure view and single mutant data analysis
Study data
| Colors: | D | E | R | H | K | S | T | N | Q | A | V | I | L | M | F | Y | W | C | G | P |
|---|
Data Distribution
Studies with similar sequences (approximate matches)
Correlation with other assays (exact sequence matches)
Relevant PDB Entries
| Structure ID | Release Date | Resolution | Structure Title |
|---|---|---|---|
| 6FT2 | 2018-03-28 | 1.25 | Structure of the periplasmic binding protein LAO-Q122A in complex with arginine. |
| 6MLP | 2019-08-07 | 1.49 | Crystal structure of the periplasmic Lysine-, Arginine-, Ornithine-binding protein (LAO) Y14A mutant from Salmonella typhimurium complexed with histidine |
| 6MLA | 2019-08-07 | 1.58 | Crystal structure of the periplasmic Lysine-, Arginine-, Ornithine-binding protein (LAO) D161A mutant from Salmonella typhimurium complexed with arginine |
| 6MLJ | 2019-08-07 | 1.6 | Crystal structure of the periplasmic Lysine-, Arginine-, Ornithine-binding protein (LAO) S70A mutant from Salmonella typhimurium complexed with arginine |
| 6MLD | 2019-08-07 | 1.66 | Crystal structure of the periplasmic Lysine-, Arginine-, Ornithine-binding protein (LAO) F52A mutant from Salmonella typhimurium |
| 6ML0 | 2019-08-07 | 1.68 | Crystal structure of the periplasmic Lysine-, Arginine-, Ornithine-binding protein (LAO) S69A mutant from Salmonella typhimurium |
| 6ML9 | 2019-08-07 | 1.69 | Crystal structure of the periplasmic Lysine-, Arginine-, Ornithine-binding protein (LAO) D30A mutant from Salmonella typhimurium complexed with arginine |
| 6MLN | 2019-08-07 | 1.72 | Crystal structure of the periplasmic Lysine-, Arginine-, Ornithine-binding protein (LAO) S72A mutant from Salmonella typhimurium complexed with arginine |
| 6MLO | 2019-08-07 | 1.72 | Crystal structure of the periplasmic Lysine-, Arginine-, Ornithine-binding protein (LAO) Y14A mutant from Salmonella typhimurium complexed with arginine |
| 6MKU | 2019-08-07 | 1.73 | Crystal structure of the periplasmic Lysine-, Arginine-, Ornithine-binding protein (LAO) D11A mutant from Salmonella typhimurium complexed with arginine |
| 1LST | 1994-06-22 | 1.8 | THREE-DIMENSIONAL STRUCTURES OF THE PERIPLASMIC LYSINE-, ARGININE-, ORNITHINE-BINDING PROTEIN WITH AND WITHOUT A LIGAND |
| 6MLE | 2019-08-07 | 1.86 | Crystal structure of the periplasmic Lysine-, Arginine-, Ornithine-binding protein (LAO) from Salmonella typhimurium complexed with arginine |
| 6MLI | 2019-08-07 | 1.88 | Crystal structure of the periplasmic Lysine-, Arginine-, Ornithine-binding protein (LAO) R77A mutant from Salmonella typhimurium complexed with histidine |
| 6MLG | 2019-08-07 | 1.89 | Crystal structure of the periplasmic Lysine-, Arginine-, Ornithine-binding protein (LAO) R77A mutant from Salmonella typhimurium complexed with arginine |
| 2LAO | 1994-06-22 | 1.9 | THREE-DIMENSIONAL STRUCTURES OF THE PERIPLASMIC LYSINE-, ARGININE-, ORNITHINE-BINDING PROTEIN WITH AND WITHOUT A LIGAND |
| 5OWF | 2018-03-21 | 1.91 | Structure of a LAO-binding protein mutant with glutamine |
| 1LAF | 1995-07-10 | 2.06 | STRUCTURAL BASES FOR MULTIPLE LIGAND SPECIFICITY OF THE PERIPLASMIC LYSINE-, ARGININE-, ORNITHINE-BINDING PROTEIN |
| 1LAH | 1995-07-10 | 2.06 | STRUCTURAL BASES FOR MULTIPLE LIGAND SPECIFICITY OF THE PERIPLASMIC LYSINE-, ARGININE-, ORNITHINE-BINDING PROTEIN |
| 1LAG | 1995-07-10 | 2.06 | STRUCTURAL BASES FOR MULTIPLE LIGAND SPECIFICITY OF THE PERIPLASMIC LYSINE-, ARGININE-, ORNITHINE-BINDING PROTEIN |
| 6MLV | 2019-08-07 | 2.08 | Crystal structure of the periplasmic Lysine-, Arginine-, Ornithine-binding protein (LAO) Y14A mutant from Salmonella typhimurium |
| 6MKX | 2019-08-07 | 2.28 | Crystal structure of the periplasmic Lysine-, Arginine-, Ornithine-binding protein (LAO) R77A mutant from Salmonella typhimurium |
| 6MKW | 2019-08-07 | 2.32 | Crystal structure of the periplasmic Lysine-, Arginine-, Ornithine-binding protein (LAO) D11A mutant from Salmonella typhimurium complexed with histidine |