Biological Assembly 1  

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

Global Symmetry: Dihedral - D3  (3D View)
Global Stoichiometry: Homo 6-mer - A6 

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

Macromolecule Content

• Total Structure Weight: 78.96 kDa 
• Atom Count: 5006 
• Modelled Residue Count: 623 
• Deposited Residue Count: 702 
• Unique protein chains: 1

4RHI

Crystal structure of SeMet-labeled wild-type T. brucei arginase-like protein in P321 space group

• PDB DOI: 10.2210/pdb4RHI/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Trypanosoma brucei brucei TREU927
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-10-02 Released: 2014-12-31 
• Deposition Author(s): Hai, Y., Barrett, M.P., Christianson, D.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 0.261 
• R-Value Work: 0.221 
• R-Value Observed: 0.223 

Literature

Crystal Structure of an Arginase-like Protein from Trypanosoma brucei That Evolved without a Binuclear Manganese Cluster.

Hai, Y., Kerkhoven, E.J., Barrett, M.P., Christianson, D.W.

(2015) Biochemistry 54: 458-471

• PubMed: 25536859 
• DOI: 10.1021/bi501366a
• Primary Citation of Related Structures:  
  4RHI, 4RHJ, 4RHK, 4RHL, 4RHM, 4RHQ


• PubMed Abstract: 
  

The X-ray crystal structure of an arginase-like protein from the parasitic protozoan Trypanosoma brucei, designated TbARG, is reported at 1.80 and 2.38 Å resolution in its reduced and oxidized forms, respectively. The oxidized form of TbARG is a disulfide-linked hexamer that retains the overall architecture of a dimer of trimers in the reduced form. Intriguingly, TbARG does not contain metal ions in its putative active site, and amino acid sequence comparisons indicate that all but one of the residues required for coordination to the catalytically obligatory binuclear manganese cluster in other arginases are substituted here with residues incapable of metal ion coordination. Therefore, the structure of TbARG is the first of a member of the arginase/deacetylase superfamily that is not a metalloprotein. Although we show that metal binding activity is easily reconstituted in TbARG by site-directed mutagenesis and confirmed in X-ray crystal structures, it is curious that this protein and its parasitic orthologues evolved away from metal binding function. Knockout of the TbARG gene from the genome demonstrated that its function is not essential to cultured bloodstream-form T. brucei, and metabolomics analysis confirmed that the enzyme has no role in the conversion of l-arginine to l-ornithine in these cells. While the molecular function of TbARG remains enigmatic, the fact that the T. brucei genome encodes only this protein and not a functional arginase indicates that the parasite must import l-ornithine from its host to provide a source of substrate for ornithine decarboxylase in the polyamine biosynthetic pathway, an active target for the development of antiparasitic drugs.

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Organizational Affiliation: 

Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania , Philadelphia, Pennsylvania 19104-6323, United States.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Arginase	A, B	351	Trypanosoma brucei brucei TREU927	Mutation(s): 0  Gene Names: Tb927.8.2020 EC: 3.5.3.1
UniProt
Find proteins for Q581Y0 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1)) Explore Q581Y0  Go to UniProtKB:  Q581Y0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 0.261 
• R-Value Work: 0.221 
• R-Value Observed: 0.223 
• Space Group: P 3 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 139.009	α = 90
b = 139.009	β = 90
c = 90.509	γ = 120

Software Package:

Software Name	Purpose
CBASS	data collection
HKL2Map	model building
PHENIX	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
HKL2Map	phasing
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-10-02 
• Released Date: 2014-12-31 
Deposition Author(s): Hai, Y., Barrett, M.P., Christianson, D.W.

Revision History  

• Version 1.0: 2014-12-31
  Type: Initial release
  
• Version 1.1: 2015-01-14
  Changes: Database references
• Version 1.2: 2015-02-04
  Changes: Database references
• Version 1.3: 2017-11-22
  Changes: Refinement description