3E9B

X-ray structure of rat arginase I-T135A mutant: the complex with BEC


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Probing the specificity determinants of amino acid recognition by arginase.

Shishova, E.Y.Di Costanzo, L.Emig, F.A.Ash, D.E.Christianson, D.W.

(2009) Biochemistry 48: 121-131

  • DOI: 10.1021/bi801911v
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Arginase is a binuclear manganese metalloenzyme that serves as a therapeutic target for the treatment of asthma, erectile dysfunction, and atherosclerosis. In order to better understand the molecular basis of inhibitor affinity, we have employed site ...

    Arginase is a binuclear manganese metalloenzyme that serves as a therapeutic target for the treatment of asthma, erectile dysfunction, and atherosclerosis. In order to better understand the molecular basis of inhibitor affinity, we have employed site-directed mutagenesis, enzyme kinetics, and X-ray crystallography to probe the molecular recognition of the amino acid moiety (i.e., the alpha-amino and alpha-carboxylate groups) of substrate l-arginine and inhibitors in the active site of arginase I. Specifically, we focus on (1) a water-mediated hydrogen bond between the substrate alpha-carboxylate and T135, (2) a direct hydrogen bond between the substrate alpha-carboxylate and N130, and (3) a direct charged hydrogen bond between the substrate alpha-amino group and D183. Amino acid substitutions for T135, N130, and D183 generally compromise substrate affinity as reflected by increased K(M) values but have less pronounced effects on catalytic function as reflected by minimal variations of k(cat). As with substrate K(M) values, inhibitor K(d) values increase for binding to enzyme mutants and suggest that the relative contribution of intermolecular interactions to amino acid affinity in the arginase active site is water-mediated hydrogen bond < direct hydrogen bond < direct charged hydrogen bond. Structural comparisons of arginase with the related binuclear manganese metalloenzymes agmatinase and proclavaminic acid amidinohydrolase suggest that the evolution of substrate recognition in the arginase fold occurs by mutation of residues contained in specificity loops flanking the mouth of the active site (especially loops 4 and 5), thereby allowing diverse guanidinium substrates to be accommodated for catalysis.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Arginase-1
A, B, C
323Rattus norvegicusMutation(s): 1 
Gene Names: Arg1
EC: 3.5.3.1
Find proteins for P07824 (Rattus norvegicus)
Go to UniProtKB:  P07824
Small Molecules
Ligands 2 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
S2C
Query on S2C

Download SDF File 
Download CCD File 
A, B, C
S-2-(BORONOETHYL)-L-CYSTEINE
C5 H13 B N O5 S
XLVRIIJULVQAMP-BYPYZUCNSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
S2CKi: 4500 nM BINDINGMOAD
S2CKi: 4500 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.216 
  • Space Group: P 32
Unit Cell:
Length (Å)Angle (°)
a = 87.505α = 90.00
b = 87.505β = 90.00
c = 100.696γ = 120.00
Software Package:
Software NamePurpose
ADSCdata collection
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-12-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance