PDBsum entry 2jdu

Lectin

PDB id: 2jdu

Contents

Protein chains

114 a.a.

Ligands

GOL ×2

SO4 ×7

MFU ×2

Metals

_CA ×4

Waters ×535

References listed in PDB file

Key reference

Title

Engineering of pa-Iil lectin from pseudomonas aeruginosa - Unravelling the role of the specificity loop for sugar preference.

Authors

J.Adam, M.Pokorná, C.Sabin, E.P.Mitchell, A.Imberty, M.Wimmerová.

Ref.

Bmc Struct Biol, 2007, 7, 36.

PubMed id

17540045

Abstract

BACKGROUND: Lectins are proteins of non-immune origin capable of binding saccharide structures with high specificity and affinity. Considering the high encoding capacity of oligosaccharides, this makes lectins important for adhesion and recognition. The present study is devoted to the PA-IIL lectin from Pseudomonas aeruginosa, an opportunistic human pathogen capable of causing lethal complications in cystic fibrosis patients. The lectin may play an important role in the process of virulence, recognizing specific saccharide structures and subsequently allowing the bacteria to adhere to the host cells. It displays high values of affinity towards monosaccharides, especially fucose--a feature caused by unusual binding mode, where two calcium ions participate in the interaction with saccharide. Investigating and understanding the nature of lectin-saccharide interactions holds a great potential of use in the field of drug design, namely the targeting and delivery of active compounds to the proper site of action. RESULTS: In vitro site-directed mutagenesis of the PA-IIL lectin yielded three single point mutants that were investigated both structurally (by X-ray crystallography) and functionally (by isothermal titration calorimetry). The mutated amino acids (22-23-24 triad) belong to the so-called specificity binding loop responsible for the monosaccharide specificity of the lectin. The mutation of the amino acids resulted in changes to the thermodynamic behaviour of the mutants and subsequently in their relative preference towards monosaccharides. Correlation of the measured data with X-ray structures provided the molecular basis for rationalizing the affinity changes. The mutations either prevent certain interactions to be formed or allow formation of new interactions--both of afore mentioned have strong effects on the saccharide preferences. CONCLUSION: Mutagenesis of amino acids forming the specificity binding loop allowed identification of one amino acid that is crucial for definition of the lectin sugar preference. Altering specificity loop amino acids causes changes in saccharide-binding preferences of lectins derived from PA-IIL, via creation or blocking possible binding interactions. This finding opens a gate towards protein engineering and subsequent protein design to refine the desired binding properties and preferences, an approach that could have strong potential for drug design.

Secondary reference #1

Title

Structural basis for oligosaccharide-Mediated adhesion of pseudomonas aeruginosa in the lungs of cystic fibrosis patients.

Authors

E.Mitchell, C.Houles, D.Sudakevitz, M.Wimmerova, C.Gautier, S.Pérez, A.M.Wu, N.Gilboa-Garber, A.Imberty.

Ref.

Nat Struct Biol, 2002, 9, 918-921. [DOI no: 10.1038/nsb865]

PubMed id

12415289

Figure 1.
Figure 1. Structure of the PA-IIL -fucose complex. Stick representation of fucose and calcium ions as space-filling models. a, Monomer of PA-IIL with numbering of -strands according to the greek-key motif (strands 1 -5). b, Dimer with chain A in blue and chain B in green. c, Two perpendicular views of the tetramer consisting of the asymmetric unit.

Figure 2.
Figure 2. Interactions of PA-IIL with calcium ions and fucose. a, Stick representation of the amino acids involved in binding. Ca^2+ coordination bonds are shown as solid orange lines; hydrogen bonds, as dashed green lines. Color coding is red, oxygen; blue, nitrogen; black, carbon; and pink, Ca^2+. b, Electrostatic surface representation (color coding from violet for negative to orange for positive) of the PA-IIL-binding site with Ca^2+ (large pink spheres) and fucose (stick model). c, Stereo view of the final 2F[o] - F[c] electron density map around the fucose molecule bound to subunit A. The density is contoured at 1.0 .

The above figures are reproduced from the cited reference with permission from Macmillan Publishers Ltd

Secondary reference #2

Title

Binding of different monosaccharides by lectin pa-Iil from pseudomonas aeruginosa: thermodynamics data correlated with X-Ray structures.

Authors

C.Sabin, E.P.Mitchell, M.Pokorná, C.Gautier, J.P.Utille, M.Wimmerová, A.Imberty.

Ref.

FEBS Lett, 2006, 580, 982-987. [DOI no: 10.1016/j.febslet.2006.01.030]

PubMed id

16438968

Figure 1.
Fig. 1. Schematic representation of the monosaccharides of interest together with numbering of ring carbons. The three hydroxyl groups involved in the coordination of calcium when complexed with PA-IIL are indicated in bold. Fig. 1. Schematic representation of the monosaccharides of interest together with numbering of ring carbons. The three hydroxyl groups involved in the coordination of calcium when complexed with PA-IIL are indicated in bold.

Figure 5.
Fig. 5. Binding sites of PA-IIL complexed with monosaccharides. Left panel: superposition of the four binding sites of the asymmetric unit. Sugar and water molecules belonging to the same monomer are drawn with the same shade of green. Coordination contacts are indicated by blue solid lines and hydrogen bonds by green dashed lines. The * symbol indicates the terminal glycine from the second monomer. Right panel: Accessible surface of the protein calculated with the MOLCAD program [25] for one binding site. (A) PA-IIL/L-Gal complex, (B) PA-IIL/Me-β-Ara complex, (C) PA-IIL/Fuc complex from PDB code 1UZV [9]. Fig. 5. Binding sites of PA-IIL complexed with monosaccharides. Left panel: superposition of the four binding sites of the asymmetric unit. Sugar and water molecules belonging to the same monomer are drawn with the same shade of green. Coordination contacts are indicated by blue solid lines and hydrogen bonds by green dashed lines. The * symbol indicates the terminal glycine from the second monomer. Right panel: Accessible surface of the protein calculated with the MOLCAD program [3][25] for one binding site. (A) PA-IIL/L-Gal complex, (B) PA-IIL/Me-β-Ara complex, (C) PA-IIL/Fuc complex from PDB code 1UZV [4][9].

The above figures are reproduced from the cited reference with permission from the Federation of European Biochemical Societies

Secondary reference #3

Title

Unusual entropy-Driven affinity of chromobacterium violaceum lectin cv-Iil toward fucose and mannose.

Authors

M.Pokorná, G.Cioci, S.Perret, E.Rebuffet, N.Kostlánová, J.Adam, N.Gilboa-Garber, E.P.Mitchell, A.Imberty, M.Wimmerová.

Ref.

Biochemistry, 2006, 45, 7501-7510. [DOI no: 10.1021/bi060214e]

PubMed id

16768446