5LSH

human lysozyme in complex with a tetrasaccharide fragment of the O-chain of LPS from Klebsiella pneumoniae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.061 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Lysozyme's lectin-like characteristics facilitates its immune defense function.

Zhang, R.Wu, L.Eckert, T.Burg-Roderfeld, M.Rojas-Macias, M.A.Lutteke, T.Krylov, V.B.Argunov, D.A.Datta, A.Markart, P.Guenther, A.Norden, B.Schauer, R.Bhunia, A.Enani, M.A.Billeter, M.Scheidig, A.J.Nifantiev, N.E.Siebert, H.C.

(2017) Q. Rev. Biophys. 50: e9-e9

  • DOI: 10.1017/S0033583517000075

  • PubMed Abstract: 
  • Interactions between human lysozyme (HL) and the lipopolysaccharide (LPS) of Klebsiella pneumoniae O1, a causative agent of lung infection, were identified by surface plasmon resonance. To characterize the molecular mechanism of this interaction, HL ...

    Interactions between human lysozyme (HL) and the lipopolysaccharide (LPS) of Klebsiella pneumoniae O1, a causative agent of lung infection, were identified by surface plasmon resonance. To characterize the molecular mechanism of this interaction, HL binding to synthetic disaccharides and tetrasaccharides representing one and two repeating units, respectively, of the O-chain of this LPS were studied. pH-dependent structural rearrangements of HL after interaction with the disaccharide were observed through nuclear magnetic resonance. The crystal structure of the HL-tetrasaccharide complex revealed carbohydrate chain packing into the A, B, C, and D binding sites of HL, which primarily occurred through residue-specific, direct or water-mediated hydrogen bonds and hydrophobic contacts. Overall, these results support a crucial role of the Glu35/Asp53/Trp63/Asp102 residues in HL binding to the tetrasaccharide. These observations suggest an unknown glycan-guided mechanism that underlies recognition of the bacterial cell wall by lysozyme and may complement the HL immune defense function.


    Organizational Affiliation

    Institute of Biochemistry, Christian-Albrechts-University,Olshausenstrasse 40, 24098 Kiel,Germany.,Pneumology, Heart-Thorax-Center Fulda,Pacelliallee 4 - 36043 Fulda,Germany.,Medical Clinic II, Justus-Liebig-University,Klinikstra├če 33, 35392 Giessen,Germany; Member of the German Center for Lung Research (DZL).,Clinic of Obstetrics, Gynecology and Andrology for Small and Large Animals,Justus-Liebig-University, Justus-Liebig-University Giessen,Frankfurter Str. 106, 35392 Giessen,Germany.,Infectious Diseases Division, Department of Medicine,King Fahad Medical City, PO Box 59046, Riyadh 11525,Kingdom of Saudi Arabia.,Laboratory of Glycoconjugate Chemistry,N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences,Leninsky prospect 47, 119991 Moscow,Russian Federation.,Department of Biophysics,Bose Institute,P-1/12 CIT Scheme VII (M), Kolkata 700054,India.,Department of Structural Biology,Institute of Zoology, Christian-Albrechts-University,Am Botanischen Garten 1-9, 24118 Kiel,Germany.,RI-B-NT Research Institute of Bioinformatics and Nanotechnology,Franziusallee 177, 24148 Kiel,Germany.,Department of Chemical and Biological Engineering,Chalmers University of Technology,41296 Gothenburg,Sweden.,Institute for Veterinary Physiology and Biochemistry, Justus-Liebig-University,Frankfurter Str.100, 35392 Giessen,Germany.,Department of Chemistry and Molecular Biology,University of Gothenburg,40530 Gothenburg,Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysozyme C
A
130Homo sapiensMutation(s): 0 
Gene Names: LYZ (LZM)
EC: 3.2.1.17
Find proteins for P61626 (Homo sapiens)
Go to Gene View: LYZ
Go to UniProtKB:  P61626
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
KTS
Query on KTS

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Download CCD File 
A
(2~{R},3~{R},4~{S},5~{R},6~{R})-2-[(2~{S},3~{R},4~{R},5~{R})-2-[(1~{R})-1,2-bis(oxidanyl)ethyl]-5-[(2~{R},3~{R},4~{S},5~{S},6~{R})-2-[(2~{S},3~{R},4~{R},5~{R})-2-[(1~{R})-1,2-bis(oxidanyl)ethyl]-4-oxidanyl-5-propoxy-oxolan-3-yl]oxy-6-(hydroxymethyl)-3,5-bis(oxidanyl)oxan-4-yl]oxy-4-oxidanyl-oxolan-3-yl]oxy-6-(hydroxymethyl)oxane-3,4,5-triol
C27 H48 O21
ZXIWHLDFCNGGIL-ZIXUGQMTSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.061 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.180 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 33.108α = 90.00
b = 56.040β = 90.00
c = 60.531γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-06-21
    Type: Initial release
  • Version 1.1: 2017-12-27
    Type: Database references