1LMQ

THE CRYSTAL STRUCTURES OF THREE COMPLEXES BETWEEN CHITOOLIGOSACCHARIDES AND LYSOZYME FROM THE RAINBOW TROUT


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Observed: 0.165 

wwPDB Validation 3D Report Full Report



Literature

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

Karlsen, S.Hough, E.

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

  • DOI: 10.1107/S0907444995005105
  • Primary Citation of Related Structures:  
    1LMQ, 1LMP, 1LMO

  • PubMed 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. Lysozyme ...

    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.


    Related Citations: 
    • The Refined Crystal Structure of Lysozyme from Rainbow Trout (Oncorhynchus Mykiss)
      Karlsen, S., Eliassen, B.E., Hansen, L.Kr., Larsen, R.L., Riise, B.W., Smalaas, A.O., Hough, E., Grinde, B.
      () To be published --: --
    • Purification and Characterization of Two Lysozymes from Rainbow Trout (Salmo Gairdneri)
      Grinde, B., Jolles, J., Jolles, P.
      (1988) Eur J Biochem 173: 269

    Organizational Affiliation

    Department of Chemistry, Institute of Mathematical and Physical Science, University of Tromsø, Norway.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
LYSOZYMEA129Oncorhynchus mykissMutation(s): 0 
EC: 3.2.1.17
Find proteins for P11941 (Oncorhynchus mykiss)
Explore P11941 
Go to UniProtKB:  P11941
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose
B
4 N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Observed: 0.165 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.58α = 90
b = 76.58β = 90
c = 54.19γ = 120
Software Package:
Software NamePurpose
MADNESdata collection
PROLSQrefinement
MADNESdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 1994-10-25 
  • Released Date: 1996-01-01 
  • Deposition Author(s): Karlsen, S., Hough, E.

Revision History 

  • Version 1.0: 1996-01-01
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2018-04-18
    Changes: Data collection, Other
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary