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 
  • R-Value Observed: 0.216 

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Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/10.1021/bi801911v
  • Primary Citation of Related Structures:  
    3E6K, 3E6V, 3E8Q, 3E8Z, 3E9B

  • 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-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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Arginase-1
A, B, C
323Rattus 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
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
S2C
Query on S2C

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B],
L [auth C]
S-2-(BORONOETHYL)-L-CYSTEINE
C5 H13 B N O5 S
XLVRIIJULVQAMP-BYPYZUCNSA-N
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
Binding Affinity Annotations 
IDSourceBinding Affinity
S2C Binding MOAD:  3E9B Ki: 4500 (nM) from 1 assay(s)
PDBBind:  3E9B Ki: 4500 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.216 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.505α = 90
b = 87.505β = 90
c = 100.696γ = 120
Software Package:
Software NamePurpose
CNSrefinement
ADSCdata collection

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-12-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.3: 2023-08-30
    Changes: Data collection, Refinement description