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:29524280
Additional Information

Structure view and single mutant data analysis

Study data

No weblogo for data of varying length.
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

Relevant UniProtKB Entries

Percent Identity Matching Chains Protein Accession Entry Name
100.0 Lysine/arginine/ornithine-binding periplasmic protein P02911 ARGT_SALTY
93.3 Lysine/arginine/ornithine-binding periplasmic protein P09551 ARGT_ECOLI