1D3V | pdb_00001d3v

CRYSTAL STRUCTURE OF THE BINUCLEAR MANGANESE METALLOENZYME ARGINASE COMPLEXED WITH 2(S)-AMINO-6-BORONOHEXANOIC ACID, AN L-ARGININE ANALOG


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.179 (Depositor) 
  • R-Value Work: 
    0.157 (Depositor) 
  • R-Value Observed: 
    0.157 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1D3V

This is version 1.3 of the entry. See complete history

Literature

Arginase-boronic acid complex highlights a physiological role in erectile function.

Cox, J.D.Kim, N.N.Traish, A.M.Christianson, D.W.

(1999) Nat Struct Biol 6: 1043-1048

  • DOI: https://doi.org/10.1038/14929
  • Primary Citation Related Structures: 
    1D3V

  • PubMed Abstract: 

    The crystal structure of the complex between the binuclear manganese metalloenzyme arginase and the boronic acid analog of L-arginine, 2(S)-amino-6-boronohexanoic acid (ABH), has been determined at 1.7 A resolution from a crystal perfectly twinned by hemihedry. ABH binds as the tetrahedral boronate anion, with one hydroxyl oxygen symmetrically bridging the binuclear manganese cluster and a second hydroxyl oxygen coordinating to Mn2+A. This binding mode mimics the transition state of a metal-activated hydroxide mechanism. This transition state structure differs from that occurring in NO biosynthesis, thereby explaining why ABH does not inhibit NO synthase. We also show that arginase activity is present in the penis. Accordingly, the tight binding and specificity of ABH allows us to probe the physiological role of arginase in modulating the NO-dependent smooth muscle relaxation required for erection. Strikingly, ABH causes significant enhancement of nonadrenergic, noncholinergic nerve-mediated relaxation of penile corpus cavernosum smooth muscle, suggesting that arginase inhibition sustains L-arginine concentrations for NO synthase activity. Therefore, human penile arginase is a potential target for therapeutic intervention in the treatment of erectile dysfunction.


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

Macromolecule Content 

  • Total Structure Weight: 70.64 kDa 
  • Atom Count: 5,015 
  • Modeled Residue Count: 616 
  • Deposited Residue Count: 646 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
PROTEIN (ARGINASE)
A, B
323Rattus norvegicusMutation(s): 0 
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
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.179 (Depositor) 
  • R-Value Work:  0.157 (Depositor) 
  • R-Value Observed: 0.157 (Depositor) 
Space Group: P 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.3α = 90
b = 91.3β = 90
c = 69.9γ = 120
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-11-17
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-07
    Changes: Data collection, Database references, Derived calculations