3KV2

HIGH RESOLUTION STRUCTURE OF HUMAN ARGINASE I IN COMPLEX WITH THE STRONG INHIBITOR N(omega)-hydroxy-nor-L-arginine (nor-NOHA)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.144 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Inhibition of human arginase I by substrate and product analogues.

Di Costanzo, L.Ilies, M.Thorn, K.J.Christianson, D.W.

(2010) Arch Biochem Biophys 496: 101-108

  • DOI: 10.1016/j.abb.2010.02.004
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Human arginase I is a binuclear manganese metalloenzyme that catalyzes the hydrolysis of L-arginine to generate L-ornithine and urea. We demonstrate that N-hydroxy-L-arginine (NOHA) binds to this enzyme with K(d)=3.6 microM, and nor-N-hydroxy-L-argin ...

    Human arginase I is a binuclear manganese metalloenzyme that catalyzes the hydrolysis of L-arginine to generate L-ornithine and urea. We demonstrate that N-hydroxy-L-arginine (NOHA) binds to this enzyme with K(d)=3.6 microM, and nor-N-hydroxy-L-arginine (nor-NOHA) binds with K(d)=517 nM (surface plasmon resonance) or K(d) approximately 50 nM (isothermal titration calorimetry). Crystals of human arginase I complexed with NOHA and nor-NOHA afford 2.04 and 1.55 A resolution structures, respectively, which are significantly improved in comparison with previously-determined structures of the corresponding complexes with rat arginase I. Higher resolution structures clarify the binding interactions of the inhibitors. Finally, the crystal structure of the complex with L-lysine (K(d)=13 microM) is reported at 1.90 A resolution. This structure confirms the importance of hydrogen bond interactions with inhibitor alpha-carboxylate and alpha-amino groups as key specificity determinants of amino acid recognition in the arginase active site.


    Organizational Affiliation

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



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Arginase-1A, B322Homo sapiensMutation(s): 0 
Gene Names: ARG1
EC: 3.5.3.1
Find proteins for P05089 (Homo sapiens)
Explore P05089 
Go to UniProtKB:  P05089
NIH Common Fund Data Resources
PHAROS  P05089
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NNH
Query on NNH

Download CCD File 
A, B
NOR-N-OMEGA-HYDROXY-L-ARGININE
C5 H12 N4 O3
KOBHCUDVWOTEKO-VKHMYHEASA-N
 Ligand Interaction
MN
Query on MN

Download CCD File 
A, B
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
NNHIC50:  2000   nM  BindingDB
NNHKd :  47.5099983215332   nM  PDBBind
NNHKd:  47.5099983215332   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.144 
  • Space Group: P 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.497α = 90
b = 90.497β = 90
c = 69.604γ = 120
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-12-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance