1RLA

THREE-DIMENSIONAL STRUCTURE OF RAT LIVER ARGINASE, THE BINUCLEAR MANGANESE METALLOENZYME OF THE UREA CYCLE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of a unique binuclear manganese cluster in arginase.

Kanyo, Z.F.Scolnick, L.R.Ash, D.E.Christianson, D.W.

(1996) Nature 383: 554-557

  • DOI: 10.1038/383554a0

  • PubMed Abstract: 
  • Each individual excretes roughly 10 kg of urea per year, as a result of the hydrolysis of arginine in the final cytosolic step of the urea cycle. This reaction allows the disposal of nitrogenous waste from protein catabolism, and is catalysed by the ...

    Each individual excretes roughly 10 kg of urea per year, as a result of the hydrolysis of arginine in the final cytosolic step of the urea cycle. This reaction allows the disposal of nitrogenous waste from protein catabolism, and is catalysed by the liver arginase enzyme. In other tissues that lack a complete urea cycle, arginase regulates cellular arginine and ornithine concentrations for biosynthetic reactions, including nitric oxide synthesis: in the macrophage, arginase activity is reciprocally coordinated with that of NO synthase to modulate NO-dependent cytotoxicity. The bioinorganic chemistry of arginase is particularly rich because this enzyme is one of very few that specifically requires a spin-coupled Mn2+-Mn2+ cluster for catalytic activity in vitro and in vivo. The 2.1 angstrom-resolution crystal structure of trimeric rat liver arginase reveals that this unique metal cluster resides at the bottom of an active-site cleft that is 15 angstroms deep. Analysis of the structure indicates that arginine hydrolysis is achieved by a metal-activated solvent molecule which symmetrically bridges the two Mn2+ ions.


    Related Citations: 
    • Crystallization and Oligomeric Structure of Rat Liver Arginase
      Kanyo, Z.F.,Chen, C.Y.,Daghigh, F.,Ash, D.E.,Christianson, D.W.
      (1992) J.Mol.Biol. 224: 1175


    Organizational Affiliation

    Department of Chemistry, University of Pennsylvania, Philadelphia 19104-6323, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ARGINASE
A, B, C
323Rattus norvegicusMutation(s): 0 
Gene Names: Arg1
EC: 3.5.3.1
Find proteins for P07824 (Rattus norvegicus)
Go to UniProtKB:  P07824
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A, B, C
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.178 
  • Space Group: P 32
Unit Cell:
Length (Å)Angle (°)
a = 88.500α = 90.00
b = 88.500β = 90.00
c = 106.200γ = 120.00
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
MOSFLMdata reduction
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-10-15
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance