PDBsum entry 1bb7

Hydrolase

PDB id: 1bb7

Contents

Protein chain

129 a.a.

Ligands

GUM

Waters ×133

References listed in PDB file

Key reference

Title

Structural studies on the binding of 4-Methylumbelliferone glycosides of chitin to rainbow trout lysozyme.

Authors

V.B.Vollan, E.Hough, S.Karlsen.

Ref.

Acta Crystallogr D Biol Crystallogr, 1999, 55, 60-66. [DOI no: 10.1107/S0907444998006623]

PubMed id

10089395

Note In the PDB file this reference is annotated as "TO BE PUBLISHED". The citation details given above were identified by an automated search of PubMed on title and author names, giving a percentage match of 95%.

Abstract

Two complexes between rainbow trout lysozyme (RBTL) and 4-methylumbelliferyl chitobioside, 4MeU-(GlcNAc)2, and chitotrioside, 4MeU-(GlcNAc)3, were produced by co-crystallization and soaking, respectively, and the crystal structures were solved at 2.0 A resolution. The results show that 4-MeU-(GlcNAc)3 binds in subsites A-D and that 4-MeU-(GlcNAc)2 binds in subsites B-D in the active-site cleft of RBTL. This agrees well with earlier crystallographic studies on the binding of oligosaccharides of chitin to RBTL, which showed that (GlcNAc)3 binds to sites B-D in RBTL and not to A-C as seen in the human and turkey egg-white lysozymes. For both complexes the 4-MeU moiety in site D has diffuse electron density and is flexible, as it is only bound to water molecules and not to the protein. Since no electron density was observed in site E, the solved structures give views of nonproductive enzyme-substrate complexes.

Figure 4.
Figure 4 Hydrogen-bonding interactions between (a) 4-MeU-(GlcNAc)[2] and (b) 4-MeU-(GlcNAc)[3] and RBTL. The complexes are illustrated with ball-and-stick models and the hydrogen bonds are shown by dotted lines. The figures were generated by using the program BOBSCRIPT (Esnouf, 1997[Esnouf, R. M. (1997). J. Mol. Graph. 15, 133-138.]).

Figure 5.
Figure 5 All figures were generated using BOBSCRIPT (Esnouf, 1997[Esnouf, R. M. (1997). J. Mol. Graph. 15, 133-138.]). (a) A superimposition of 4-MeU-(GlcNAc)[2] (blue) on 4-MeU-(GlcNAc)[3] (red) in the active-site cleft of RBTL. The protein models in the former and latter complexes are coloured green and purple, respectively. (b) A superimposition of RBTL-4-MeU-(GlcNAc)[3] (purple/red) and RBTL-(GlcNAc)[4] (green/blue) (Karlsen & Hough, 1995[Karlsen, S. & Hough, E. (1995). Acta Cryst. D51, 962-978.]). (c) A superimposition of RBTL-4-MeU-(GlcNAc)[3] (purple/red) and RBTL-bulgecin (green/blue) (Karlsen & Hough, 1996[Karlsen, S. & Hough, E. (1996). Acta Cryst. D52, 115-123.]).

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (1999, 55, 60-66) copyright 1999.

Secondary reference #1

Title

Crystal structures of three complexes between chito-Oligosaccharides and lysozyme from the rainbow trout. How distorted is the NAG sugar in site d?

Authors

S.Karlsen, E.Hough.

Ref.

Acta Crystallogr D Biol Crystallogr, 1995, 51, 962-978. [DOI no: 10.1107/S0907444995005105]

PubMed id

15299765

Figure 3.
ig. 3. Fo-Fc omit map contoured at 0.12 e A -3 (2~r) for the (NAG)4 molecule bound in the ctive-site cleft of RBTL. The oligosaccharide was omitted from the oordinate file.

Figure 6.
Fig. 6. Fo -Fc omit map contoured at 0.12e/~ -3 for the refined NAG ring in site D (green). A model of a pyranose ring (orange) with sofa conformaton is included for comparisn.

Figure 7.
Fig. 7. Hydrogen-bonding inter- actions between protein atoms and sugar residues within sites A to D in RBTL. Lysozyme structure is shown with thin lines, sugar residues with thick lines and hydrogen bonds with broken lines. Water molecules are depicted with crosses.

Figure 8.
Fig. 8. Superimpostions of (a) the (NAG)2 (green) and (b) the (NAG)3 (green) molecule on (NAG)4 (red) in sites B and C and B, C and D of RBTL, respectively.

Figure 9.
Fig. 9. (a) A superimposition of GM (NAM-NAG-NAM) (green) bound to HEWL (red) on (NAG) 4 (orange) in RBTL (blue). (b) A closer view of the saccharides in the C and D site of HEWL and RBTL (same colours as in (a). (c) A superimposition of 8-1actone (green) on (NAG) 4 (red) in sites A to D in RBTL.

Figure 10.
Fig. 10. Proposed binding ofa hexa- saccharide (thick lines) of chitin in the active-site cleft of RBTL. The in sites A to D have the crystallogmphically determined positions.

Figure 11.
Fig. 11. Co-drawing of the RBTL-(NAG)4 complex coloured according to differences in temperature factors etween the native and he liganded form of the enzyme. The molecule is coloured as follows: .AB <-3 A2 (blue), -3 ,~2 < ~B < 3 A2 (light blue), 3 ,~2 < AB < 12 A2 (light red) and AB > 12 ,~2(yelow). Residues that interact directly with the ligand are marked in light green and the saccharide is depicted with blue van dr Waals spheres.

Figure 12.
Fig. 12. R.m.s. diferences along the main-chain atoms between the native and the structure of RBTL with bound (NAG)4.

Figure 13.
Fig. 13. Ordered watcr molecules within thc D binding sitc in the activc-site cleft of unligandcd (a) and (NAG)4-bound (b) RBTL. Watcr molecules arc marked with crosses.

The above figures are reproduced from the cited reference with permission from the IUCr

Secondary reference #2

Title

Refined crystal structure of lysozyme from the rainbow trout (oncorhynchus mykiss).

Authors

S.Karlsen, B.E.Eliassen, L.K.Hansen, R.L.Larsen, B.W.Riise, A.O.Smalås, E.Hough, B.Grinde.

Ref.

Acta Crystallogr D Biol Crystallogr, 1995, 51, 354-367. [DOI no: 10.1107/S0907444994010929]

PubMed id

15299303

Figure 1.
Fig. 1. Effect on R factor of rotation in (a) or, (b) fl and (c) y and translations in (d) x, (e) y and (f) z around the correct solutions. For ach rotation or translation the fve oter parameters were kept onstant.

Figure 8.
Fig. 8. The environment of the catalytic residue. Hydrogen bonds are shown as thin, broken lines. Only side chains critical to the present discussion are shown.

The above figures are reproduced from the cited reference with permission from the IUCr