PDBsum entry 1lmo

Hydrolase (o-glycosyl)

PDB id: 1lmo

Contents

Protein chain

129 a.a. *

Ligands

NAG-NAG

Waters ×113

* Residue conservation analysis

PDB id:

1lmo

Name:

Hydrolase (o-glycosyl)

Title:

The crystal structures of three complexes between chitooligosaccharides and lysozyme from the rainbow trout

Structure:

Lysozyme. Chain: a. Synonym: mucopeptide n-acetylmuramylhydrolase. Ec: 3.2.1.17

Source:

Oncorhynchus mykiss. Rainbow trout. Organism_taxid: 8022. Organ: kidney

Biol. unit:

Dimer (from PQS)

Resolution:

1.80Å R-factor: 0.166

Authors:

S.Karlsen,E.Hough

Key ref:

S.Karlsen and E.Hough (1995). Crystal structures of three complexes between chito-oligosaccharides and lysozyme from the rainbow trout. How distorted is the NAG sugar in site D? Acta Crystallogr D Biol Crystallogr, 51, 962-978. PubMed id: 15299765 DOI: 10.1107/S0907444995005105

Date:

25-Oct-94 Release date: 01-Jan-96

Protein chain

P11941  (LYSC2_ONCMY) -  Lysozyme C II from Oncorhynchus mykiss

Seq: 144 a.a.

Struc: 129 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.3.2.1.17 - lysozyme.
• Reaction: Hydrolysis of the 1,4-beta-linkages between N-acetyl-D-glucosamine and N-acetylmuramic acid in peptidoglycan heteropolymers of the prokaryotes cell walls.

DOI no: 10.1107/S0907444995005105

Acta Crystallogr D Biol Crystallogr 51:962-978 (1995)

PubMed id: 15299765

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

S.Karlsen, E.Hough.

ABSTRACT

Like all c-type lysozymes, those from rainbow trout act as 1,4-beta-acetyl-muramidases to destroy bacteria by cleaving the polysaccharide chains of alternating N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM) units in the cell walls. Lysozymes also hydrolyse chitin, the analogous N-acetylglucosamine polymer. The rainbow trout enzymes have been shown to be particularly effective in bacterial defence. We have determined the crystal structures of three complexes between rainbow trout lysozyme (RBTL) and the chito-oligosaccharides (NAG)(2), (NAG)(3) and (NAG)(4) to resolutions of 1.8, 2.0 and 1.6 A, respectively. Crystals of these complexes were obtained by co-crystallization, and intensity data were collected on a FAST area detector system. Refinement and model building gave final R values of 16.6, 15.9 and 16.5% for the di-, tri- and tetrasaccharide complexes, respectively. The results show that the chito-oligosaccharides bind to sites A, B and C as previously observed for complexes between the hen egg-white lysozyme (HEWL) and a variety of saccharides. The NAG ring in site D is not bound so deeply and is only slightly distorted towards a half-chair conformation as observed for the equivalent NAM residue in HEWL. From our results, there is reason to question the position and the degree of strain of the D saccharide and the mode of binding and importance of two saccharides in sites E and F for correct orientation of sugar D and effective hydrolysis of a productive substrate-lysozyme complex. Simple model building study from our structures implies a 'left-sided' binding mode of (NAG)(6) in the lower part of the active site of RBTL.

Selected figure(s)

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 reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (1995, 51, 962-978) copyright 1995.

Figures were selected by an automated process.