1P8P

Structural and Functional Importance of First-Shell Metal Ligands in the Binuclear Manganese Cluster of Arginase I.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.237 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structural and functional importance of first-shell metal ligands in the binuclear manganese cluster of arginase I

Cama, E.Emig, F.A.Ash, D.E.Christianson, D.W.

(2003) Biochemistry 42: 7748-7758

  • DOI: 10.1021/bi030074y
  • Primary Citation of Related Structures:  
    1P8M, 1P8N, 1P8O, 1P8P, 1P8Q, 1P8R, 1P8S

  • PubMed Abstract: 
  • Arginase is a binuclear manganese metalloenzyme that hydrolyzes l-arginine to form l-ornithine and urea. The three-dimensional structures of D128E, D128N, D232A, D232C, D234E, H101N, and H101E arginases I have been determined by X-ray crystallographic methods to elucidate the roles of the first-shell metal ligands in the stability and catalytic activity of the enzyme ...

    Arginase is a binuclear manganese metalloenzyme that hydrolyzes l-arginine to form l-ornithine and urea. The three-dimensional structures of D128E, D128N, D232A, D232C, D234E, H101N, and H101E arginases I have been determined by X-ray crystallographic methods to elucidate the roles of the first-shell metal ligands in the stability and catalytic activity of the enzyme. This work represents the first structure-based dissection of the binuclear manganese cluster using site-directed mutagenesis and X-ray crystallography. Substitution of the metal ligands compromises the catalytic activity of the enzyme, either by the loss or disruption of the metal cluster or the nucleophilic metal-bridging hydroxide ion. However, the substitution of the metal ligands or the reduction of Mn(2+)(A) or Mn(2+)(B) occupancy does not compromise enzyme-substrate affinity as reflected by K(M), which remains relatively invariant across this series of arginase variants. This implicates a nonmetal binding site for substrate l-arginine in the precatalytic Michaelis complex, as proposed based on analysis of the native enzyme structure (Kanyo, Z. F., Scolnick, L. R., Ash, D. E., and Christianson, D. W. (1996) Nature 383, 554-557).


    Related Citations: 
    • ALTERING THE BINUCLEAR MANGANESE CLUSTER OF ARGINASE DIMINISHES THERMOSTABILITY AND CATALYTIC FUNCTION
      Scolnick, L.R., Kanyo, Z.F., Cavalli, C.R., Ash, D.E., Christianson, D.W.
      (1997) Biochemistry 36: 10558

    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): 1 
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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.237 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89α = 90
b = 89β = 90
c = 115.4γ = 120
Software Package:
Software NamePurpose
CNSrefinement
CCP4data scaling
AMoREphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-06-17
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Advisory, Refinement description
  • Version 1.4: 2021-10-27
    Changes: Advisory, Database references, Derived calculations