Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 64.16 kDa 
• Atom Count: 4447 
• Modelled Residue Count: 562 
• Deposited Residue Count: 574 
• Unique protein chains: 1

8D27

Arginase Domain of Ornithine Decarboxylase/Arginase from Fusobacterium nucleatum

• PDB DOI: 10.2210/pdb8D27/pdb

• Classification: HYDROLASE
• Organism(s): Fusobacterium nucleatum subsp. nucleatum ATCC 25586
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-05-27 Released: 2022-07-06 
• Deposition Author(s): Chan, A.C., Kolesnikov, M., Murphy, M.E.
• Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.212 
• R-Value Work: 0.180 
• R-Value Observed: 0.194 

Literature

Sequence Divergence in the Arginase Domain of Ornithine Decarboxylase/Arginase in Fusobacteriacea Leads to Loss of Function in Oral Associated Species.

Mothersole, R.G., Kolesnikov, M., Chan, A.C.K., Oduro, E., Murphy, M.E.P., Wolthers, K.R.

(2022) Biochemistry 61: 1378-1391

• PubMed: 35732022 
• DOI: 10.1021/acs.biochem.2c00197
• Primary Citation of Related Structures:  
  8D27


• PubMed Abstract: 
  

A number of species within the Fusobacteriaceae family of Gram-negative bacteria uniquely encode for an ornithine decarboxylase/arginase (ODA) that ostensibly channels l-ornithine generated by hydrolysis of l-arginine to putrescine formation. However, two aspartate residues required for coordination to a catalytically obligatory manganese cluster of arginases are substituted for a serine and an asparagine. Curiously, these natural substitutions occur only in a clade of Fusobacterium species that inhabit the oral cavity. Herein, we expressed and isolated full-length ODA from the opportunistic oral pathogen Fusobacterium nucleatum along with the individual arginase and ornithine decarboxylase components. The crystal structure of the arginase domain reveals that it adopts the classical α/β arginase-fold, but metal ions are absent in the active site. As expected, the ureohydrolase activity with l-arginine was not detected for wild-type ODA or the isolated arginase domain. However, engineering of the complete metal coordination environment through site-directed mutagenesis restored Mn ²⁺ binding capacity and arginase activity, although the catalytic efficiency for l-arginine was low (60-100 M ^-1 s ^-1 ). Full-length ODA and the isolated ODC component were able to decarboxylate both l-ornithine and l-arginine to form putrescine and agmatine, respectively, but k _cat / K _M of l-ornithine was ∼20-fold higher compared to l-arginine. We discuss environmental conditions that may have led to the natural selection of an inactive arginase in the oral associated species of Fusobacterium .

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Organizational Affiliation: 

Department of Chemistry, University of British Columbia, Okanagan Campus, 3247 University Way, Kelowna V1V 1V7, Canada.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Arginase	A, B	287	Fusobacterium nucleatum subsp. nucleatum ATCC 25586	Mutation(s): 0  Gene Names: FN0501
UniProt
Find proteins for Q8RG18 (Fusobacterium nucleatum subsp. nucleatum (strain ATCC 25586 / DSM 15643 / BCRC 10681 / CIP 101130 / JCM 8532 / KCTC 2640 / LMG 13131 / VPI 4355)) Explore Q8RG18  Go to UniProtKB:  Q8RG18

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.212 
• R-Value Work: 0.180 
• R-Value Observed: 0.194 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.818	α = 90
b = 78.217	β = 90.03
c = 73.53	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2022-05-27 
• Released Date: 2022-07-06 
Deposition Author(s): Chan, A.C., Kolesnikov, M., Murphy, M.E.

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Funding Organization	Location	Grant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	--

Revision History  

• Version 1.0: 2022-07-06
  Type: Initial release
  
• Version 1.1: 2022-07-13
  Changes: Database references