3LP7

Crystal structure of Human Arginase I in complex with inhibitor N(omega)-hydroxy-L-arginine (NOHA), 2.04A Resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.123 

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
  • Primary Citation of Related Structures:  

  • 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-1
A, B
322Homo sapiensMutation(s): 0 
Gene Names: ARG1
EC: 3.5.3.1
Find proteins for P05089 (Homo sapiens)
Go to Gene View: ARG1
Go to UniProtKB:  P05089
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A, B
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
HAR
Query on HAR

Download SDF File 
Download CCD File 
A, B
N-OMEGA-HYDROXY-L-ARGININE
C6 H14 N4 O3
FQWRAVYMZULPNK-BYPYZUCNSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
HARKd: 3600 nM BINDINGMOAD
HARKd: 3600 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.123 
  • Space Group: P 3
Unit Cell:
Length (Å)Angle (°)
a = 90.680α = 90.00
b = 90.680β = 90.00
c = 69.820γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
CNSrefinement
ADSCdata collection
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-02-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance