1T4P

Arginase-dehydro-ABH complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.264 
  • R-Value Observed: 0.264 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Inhibitor coordination interactions in the binuclear manganese cluster of arginase

Cama, E.Pethe, S.Boucher, J.-L.Han, S.Emig, F.A.Ash, D.E.Viola, R.E.Mansuy, D.Christianson, D.W.

(2004) Biochemistry 43: 8987-8999

  • DOI: 10.1021/bi0491705
  • Primary Citation of Related Structures:  
    1T4P, 1T4R, 1T4S, 1T4T, 1T5G

  • PubMed Abstract: 
  • Arginase is a manganese metalloenzyme that catalyzes the hydrolysis of L-arginine to form L-ornithine and urea. The structure and stability of the binuclear manganese cluster are critical for catalytic activity as it activates the catalytic nucleophile, metal-bridging hydroxide ion, and stabilizes the tetrahedral intermediate and its flanking states ...

    Arginase is a manganese metalloenzyme that catalyzes the hydrolysis of L-arginine to form L-ornithine and urea. The structure and stability of the binuclear manganese cluster are critical for catalytic activity as it activates the catalytic nucleophile, metal-bridging hydroxide ion, and stabilizes the tetrahedral intermediate and its flanking states. Here, we report X-ray structures of a series of inhibitors bound to the active site of arginase, and each inhibitor exploits a different mode of coordination with the Mn(2+)(2) cluster. Specifically, we have studied the binding of fluoride ion (F(-); an uncompetitive inhibitor) and L-arginine, L-valine, dinor-N(omega)-hydroxy-L-arginine, descarboxy-nor-N(omega)-hydroxy-L-arginine, and dehydro-2(S)-amino-6-boronohexanoic acid. Some inhibitors, such as fluoride ion, dinor-N(omega)-hydroxy-L-arginine, and dehydro-2(S)-amino-6-boronohexanoic acid, cause the net addition of one ligand to the Mn(2+)(2) cluster. Other inhibitors, such as descarboxy-nor-N(omega)-hydroxy-L-arginine, simply displace the metal-bridging hydroxide ion of the native enzyme and do not cause any net change in the metal coordination polyhedra. The highest affinity inhibitors displace the metal-bridging hydroxide ion (and sometimes occupy a Mn(2+)(A) site found vacant in the native enzyme) and maintain a conserved array of hydrogen bonds with their alpha-amino and -carboxylate groups.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Arginase 1A, B, C314Rattus norvegicusMutation(s): 0 
Gene Names: Arg1
EC: 3.5.3.1
UniProt
Find proteins for P07824 (Rattus norvegicus)
Explore P07824 
Go to UniProtKB:  P07824
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07824
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2BH
Query on 2BH

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B],
L [auth C]
[(1E,5S)-5-AMINO-5-CARBOXYPENT-1-ENYL](TRIHYDROXY)BORATE(1-)
C6 H13 B N O5
CCCYGXMAMSUXAV-FYTLMZHYSA-N
 Ligand Interaction
MN
Query on MN

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.264 
  • R-Value Observed: 0.264 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.4α = 90
b = 88.4β = 90
c = 110.52γ = 120
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-04-12
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance