1WVA

Crystal structure of human arginase I from twinned crystal

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.150 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Crystal structure of human arginase I at 1.29 A resolution and exploration of inhibition in the immune response

Di Costanzo, L., Sabio, G., Mora, A., Rodriguez, P.C., Ochoa, A.C., Centeno, F., Christianson, D.W.

(2005) Proc.Natl.Acad.Sci.Usa 102: 13058-13063

  • DOI: 10.1073/pnas.0504027102
  • Primary Citation of Related Structures:  
  • Also Cited By: 3SJT

  • PubMed Abstract: 

    • Human arginase I is a potential target for therapeutic intervention in diseases linked to compromised l-arginine homeostasis. Here, we report high-affinity binding of the reaction coordinate analogue inhibitors 2(S)-amino-6-boronohexanoic acid (ABH, ...

    Human arginase I is a potential target for therapeutic intervention in diseases linked to compromised l-arginine homeostasis. Here, we report high-affinity binding of the reaction coordinate analogue inhibitors 2(S)-amino-6-boronohexanoic acid (ABH, Kd = 5 nM) and S-(2-boronoethyl)-l-cysteine (BEC, Kd = 270 nM) to human arginase I, and we report x-ray crystal structures of the respective enzyme-inhibitor complexes at 1.29- and 1.94-A resolution determined from crystals twinned by hemihedry. The ultrahigh-resolution structure of the human arginase I-ABH complex yields an unprecedented view of the binuclear manganese cluster and illuminates the structural basis for nanomolar affinity: bidentate inner-sphere boronate-manganese coordination interactions and fully saturated hydrogen bond networks with inhibitor alpha-amino and alpha-carboxylate groups. These interactions are therefore implicated in the stabilization of the transition state for l-arginine hydrolysis. Electron density maps also reveal that active-site residue H141 is protonated as the imidazolium cation. The location of H141 is such that it could function as a general acid to protonate the leaving amino group of l-ornithine during catalysis, and this is a revised mechanistic proposal for arginase. This work serves as a foundation for studying the structural and chemical biology of arginase I in the immune response, and we demonstrate the inhibition of arginase activity by ABH in human and murine myeloid cells.

    Related Citations: 
    • Human arginase II: crystal structure and physiological role in male and female sexual arousal
      Cama, E.,Colleluori, D.M.,Emig, F.A.,Shin, H.,Kim, S.W.,Kim, N.N.,Traish, A.M.,Ash, D.E.,Christianson, D.W.
      (2003) Biochemistry 42: 8445

    Organizational Affiliation: 

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Arginase 1
A, B
322Homo sapiensMutation(s): 0 
Gene Names: ARG1
EC: 3.5.3.1
Find proteins for P05089 (Homo sapiens)
Go to Gene View: ARG1
Go to UniProtKB:  P05089
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN
Download SDF File 
Download CCD File 
A, B
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
S2C
Query on S2C
Download SDF File 
Download CCD File 
A, B
S-2-(BORONOETHYL)-L-CYSTEINE
C5 H13 B N O5 S
XLVRIIJULVQAMP-BYPYZUCNSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
S2CKd: 270 nM BINDINGMOAD
S2CKd: 270 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.150 
  • Space Group: P 3
Unit Cell:
Length (Å)Angle (°)
a = 90.602α = 90.00
b = 90.602β = 90.00
c = 69.311γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
CCP4data scaling
HKL-2000data collection
SCALAdata scaling
CNSrefinement
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-09-06
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance