7TVP

Viral AMG chitosanase V-Csn, E157Q mutant, chitotriose complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.132 
  • R-Value Observed: 0.134 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural characterization of a soil viral auxiliary metabolic gene product - a functional chitosanase.

Wu, R.Smith, C.A.Buchko, G.W.Blaby, I.K.Paez-Espino, D.Kyrpides, N.C.Yoshikuni, Y.McDermott, J.E.Hofmockel, K.S.Cort, J.R.Jansson, J.K.

(2022) Nat Commun 13: 5485-5485

  • DOI: https://doi.org/10.1038/s41467-022-32993-8
  • Primary Citation of Related Structures:  
    7TVL, 7TVM, 7TVN, 7TVO, 7TVP

  • PubMed Abstract: 

    Metagenomics is unearthing the previously hidden world of soil viruses. Many soil viral sequences in metagenomes contain putative auxiliary metabolic genes (AMGs) that are not associated with viral replication. Here, we establish that AMGs on soil viruses actually produce functional, active proteins. We focus on AMGs that potentially encode chitosanase enzymes that metabolize chitin - a common carbon polymer. We express and functionally screen several chitosanase genes identified from environmental metagenomes. One expressed protein showing endo-chitosanase activity (V-Csn) is crystalized and structurally characterized at ultra-high resolution, thus representing the structure of a soil viral AMG product. This structure provides details about the active site, and together with structure models determined using AlphaFold, facilitates understanding of substrate specificity and enzyme mechanism. Our findings support the hypothesis that soil viruses contribute auxiliary functions to their hosts.


  • Organizational Affiliation

    Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Viral chitosanase V-Csn E157Q mutant chitotriose complex225unclassified sequencesMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-amino-2-deoxy-beta-D-glucopyranose-(1-4)-2-amino-2-deoxy-beta-D-glucopyranose-(1-4)-2-amino-2-deoxy-beta-D-glucopyranose
B
3N/A
Glycosylation Resources
GlyTouCan:  G36121RO
GlyCosmos:  G36121RO
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.132 
  • R-Value Observed: 0.134 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.939α = 90
b = 47.421β = 97.83
c = 45.402γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Energy (DOE, United States)United StatesFWP 70880

Revision History  (Full details and data files)

  • Version 1.0: 2022-10-05
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Refinement description