6T6C

Complex with chitin oligomer of C-type lysozyme from the upper gastrointestinal tract of Opisthocomus hoatzin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.134 
  • R-Value Work: 0.108 

wwPDB Validation 3D Report Full Report



Literature

The C-Type Lysozyme from the upper Gastrointestinal Tract ofOpisthocomus hoatzin,the Stinkbird.

Taylor, E.J.Skjot, M.Skov, L.K.Klausen, M.De Maria, L.Gippert, G.P.Turkenburg, J.P.Davies, G.J.Wilson, K.S.

(2019) Int J Mol Sci 20

  • DOI: 10.3390/ijms20225531
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Muramidases/lysozymes are important bio-molecules, which cleave the glycan backbone in the peptidoglycan polymer found in bacterial cell walls. The glycoside hydrolase (GH) family 22 C-type lysozyme, from the folivorous bird Opisthocomus hoazin < ...

    Muramidases/lysozymes are important bio-molecules, which cleave the glycan backbone in the peptidoglycan polymer found in bacterial cell walls. The glycoside hydrolase (GH) family 22 C-type lysozyme, from the folivorous bird Opisthocomus hoazin (stinkbird), was expressed in Aspergillus oryzae , and a set of variants was produced. All variants were enzymatically active, including those designed to probe key differences between the Hoatzin enzyme and Hen Egg White lysozyme. Four variants showed improved thermostability at pH 4.7, compared to the wild type. The X-ray structure of the enzyme was determined in the apo form and in complex with chitin oligomers. Bioinformatic analysis of avian GH22 amino acid sequences showed that they separate out into three distinct subgroups (chicken-like birds, sea birds and other birds). The Hoatzin is found in the "other birds" group and we propose that this represents a new cluster of avian upper-gut enzymes.


    Organizational Affiliation

    Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, UK.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysozyme C
A
128Opisthocomus hoazinMutation(s): 1 
Gene Names: LYZ
EC: 3.2.1.17
Find proteins for Q91159 (Opisthocomus hoazin)
Go to UniProtKB:  Q91159
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.134 
  • R-Value Work: 0.108 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.051α = 90
b = 55.008β = 90
c = 65.829γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
Cootmodel building

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Royal SocietyUnited Kingdom--

Revision History 

  • Version 1.0: 2019-11-20
    Type: Initial release
  • Version 2.0: 2019-11-27
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary