7TVM | pdb_00007tvm

Viral AMG chitosanase V-Csn, apo structure, crystal form 2

• PDB DOI: https://doi.org/10.2210/pdb7TVM/pdb

• Classification: HYDROLASE
• Organism(s): unclassified sequences
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-02-05 Released: 2022-10-05 
• Deposition Author(s): Smith, C.A., Wu, R., Buchko, G.W., Cort, J.R., Hofmockel, K.S., Jansson, J.K.
• Funding Organization(s): Department of Energy (DOE, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 
  0.174 (Depositor), 0.175 (DCC) 
• R-Value Work: 
  0.143 (Depositor), 0.144 (DCC) 
• R-Value Observed: 
  0.144 (Depositor) 

Starting Model: experimental

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

• PubMed: 36123347 
• DOI: https://doi.org/10.1038/s41467-022-32993-8
• Primary Citation 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.

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Organizational Affiliation: 
• Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA.
Stanford Synchrotron Radiation Light source, Stanford University, Menlo Park, CA, USA.
School of Molecular Biosciences, Washington State University, Pullman, WA, USA.
US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
Mammoth Biosciences, Brisbane, CA, USA.
Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR, USA.
Institute of Biological Chemistry, Washington State University, Pullman, WA, USA.
Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 47.99 kDa 
• Atom Count: 4,016 
• Modeled Residue Count: 446 
• Deposited Residue Count: 448 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Viral chitosanase V-Csn	A, B	224	unclassified sequences	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	C [auth A], D [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free:  0.174 (Depositor), 0.175 (DCC) 
• R-Value Work:  0.143 (Depositor), 0.144 (DCC) 
• R-Value Observed: 0.144 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 163.295	α = 90
b = 46.001	β = 92.3
c = 73.556	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-10-05 
Deposition Author(s): Smith, C.A., Wu, R., Buchko, G.W., Cort, J.R., Hofmockel, K.S., Jansson, J.K.

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Funding Organization	Location	Grant Number
Department of Energy (DOE, United States)	United States	FWP 70880

Revision History  

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