5HJ9

Crystal structure of Leishmania mexicana arginase in complex with inhibitor ABHPE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.28 Å
  • R-Value Free: 0.159 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.151 

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This is version 1.3 of the entry. See complete history


Literature

Crystal structures of Leishmania mexicana arginase complexed with alpha , alpha-disubstituted boronic amino-acid inhibitors.

Hai, Y.Christianson, D.W.

(2016) Acta Crystallogr F Struct Biol Commun 72: 300-306

  • DOI: 10.1107/S2053230X16003630
  • Primary Citation of Related Structures:  
    5HJ9, 5HJA

  • PubMed Abstract: 
  • Leishmania arginase is a potential drug target for the treatment of leishmaniasis because this binuclear manganese metalloenzyme initiates de novo polyamine biosynthesis by catalyzing the hydrolysis of L-arginine to generate L-ornithine and urea. The product L-ornithine subsequently undergoes decarboxylation to yield putrescine, which in turn is utilized for spermidine biosynthesis ...

    Leishmania arginase is a potential drug target for the treatment of leishmaniasis because this binuclear manganese metalloenzyme initiates de novo polyamine biosynthesis by catalyzing the hydrolysis of L-arginine to generate L-ornithine and urea. The product L-ornithine subsequently undergoes decarboxylation to yield putrescine, which in turn is utilized for spermidine biosynthesis. Polyamines such as spermidine are essential for the growth and survival of the parasite, so inhibition of enzymes in the polyamine-biosynthetic pathway comprises an effective strategy for treating parasitic infections. To this end, two X-ray crystal structures of L. mexicana arginase complexed with α,α-disubstituted boronic amino-acid inhibitors based on the molecular scaffold of 2-(S)-amino-6-boronohexanoic acid are now reported. Structural comparisons with human and parasitic arginase complexes reveal interesting differences in the binding modes of the additional α-substituents, i.e. the D side chains, of these inhibitors. Subtle differences in the three-dimensional contours of the outer active-site rims among arginases from different species lead to different conformations of the D side chains and thus different inhibitor-affinity trends. The structures suggest that it is possible to maintain affinity while fine-tuning intermolecular interactions of the D side chain of α,α-disubstituted boronic amino-acid inhibitors in the search for isozyme-specific and species-specific arginase inhibitors.


    Organizational Affiliation

    Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ArginaseA330Leishmania mexicanaMutation(s): 0 
Gene Names: ARG
EC: 3.5.3.1
UniProt
Find proteins for Q6TUJ5 (Leishmania mexicana)
Explore Q6TUJ5 
Go to UniProtKB:  Q6TUJ5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6TUJ5
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
X7A
Query on X7A

Download Ideal Coordinates CCD File 
D [auth A][(5R)-5-amino-5-carboxy-7-(piperidin-1-yl)heptyl](trihydroxy)borate(1-)
C13 H28 B N2 O5
SCRPJEVETAWLOZ-CYBMUJFWSA-N
 Ligand Interaction
PGE
Query on PGE

Download Ideal Coordinates CCD File 
J [auth A],
K [auth A]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
F [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
I [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MN
Query on MN

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.28 Å
  • R-Value Free: 0.159 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.151 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.092α = 90
b = 89.092β = 90
c = 113.6γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
CBASSdata collection
HKL-2000data reduction
PHASERphasing
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM 49758

Revision History  (Full details and data files)

  • Version 1.0: 2016-04-13
    Type: Initial release
  • Version 1.1: 2017-09-13
    Changes: Author supporting evidence, Derived calculations
  • Version 1.2: 2018-04-18
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 1.3: 2019-12-25
    Changes: Author supporting evidence, Derived calculations, Structure summary