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 6ZMV | pdb_00006zmv

Structure of muramidase from Trichobolus zukalii


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 
    0.143 (Depositor), 0.143 (DCC) 
  • R-Value Work: 
    0.104 (Depositor), 0.104 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6ZMV

This is version 1.3 of the entry. See complete history. 

Literature

Fungal GH25 muramidases: New family members with applications in animal nutrition and a crystal structure at 0.78 angstrom resolution.

Moroz, O.V., Blagova, E., Taylor, E., Turkenburg, J.P., Skov, L.K., Gippert, G.P., Schnorr, K.M., Ming, L., Ye, L., Klausen, M., Cohn, M.T., Schmidt, E.G.W., Nymand-Grarup, S., Davies, G.J., Wilson, K.S.

(2021) PLoS One 16: e0248190-e0248190

  • DOI: https://doi.org/10.1371/journal.pone.0248190
  • Primary Citation Related Structures: 
    6ZM8, 6ZMV

  • PubMed Abstract: 

    Muramidases/lysozymes hydrolyse the peptidoglycan component of the bacterial cell wall. They are found in many of the glycoside hydrolase (GH) families. Family GH25 contains muramidases/lysozymes, known as CH type lysozymes, as they were initially discovered in the Chalaropsis species of fungus. The characterized enzymes from GH25 exhibit both β-1,4-N-acetyl- and β-1,4-N,6-O-diacetylmuramidase activities, cleaving the β-1,4-glycosidic bond between N-acetylmuramic acid (NAM) and N-acetylglucosamine (NAG) moieties in the carbohydrate backbone of bacterial peptidoglycan. Here, a set of fungal GH25 muramidases were identified from a sequence search, cloned and expressed and screened for their ability to digest bacterial peptidoglycan, to be used in a commercial application in chicken feed. The screen identified the enzyme from Acremonium alcalophilum JCM 736 as a suitable candidate for this purpose and its relevant biochemical and biophysical and properties are described. We report the crystal structure of the A. alcalophilum enzyme at atomic, 0.78 Å resolution, together with that of its homologue from Trichobolus zukalii at 1.4 Å, and compare these with the structures of homologues. GH25 enzymes offer a new solution in animal feed applications such as for processing bacterial debris in the animal gut.


  • Organizational Affiliation: 
    • Department of Chemistry, Structural Biology Laboratory, The University of York, York, United Kingdom.

Macromolecule Content 

  • Total Structure Weight: 46.01 kDa 
  • Atom Count: 4,047 
  • Modeled Residue Count: 414 
  • Deposited Residue Count: 414 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
muramidase
A, B
207Trichobolus zukaliiMutation(s): 0 
EC: 3.2.1.17
UniProt
Find proteins for A0A7S6G7I6 (Trichobolus zukalii)
Explore A0A7S6G7I6 
Go to UniProtKB:  A0A7S6G7I6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A7S6G7I6
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4

Query on SO4



Download:Ideal Coordinates CCD File
G [auth A],
L [auth B],
M [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
C [auth A]
D [auth A]
E [auth A]
F [auth A]
H [auth B]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
H [auth B],
I [auth B],
J [auth B],
K [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free:  0.143 (Depositor), 0.143 (DCC) 
  • R-Value Work:  0.104 (Depositor), 0.104 (DCC) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.398α = 97.076
b = 48.582β = 99.531
c = 55.737γ = 98.15
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-14
    Type: Initial release
  • Version 1.1: 2022-01-26
    Changes: Advisory, Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Derived calculations, Refinement description
  • Version 1.3: 2024-11-06
    Changes: Structure summary